GTN Feedback

Aggregation of feedback submitted since 2018-09 using the embed feedback form at the bottom of tutorials. Thank you everyone who submitted feedback!

Overall

2023 responses
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By topic

Assembly

71 responses
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5 responses
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Mar 25, 2019 Easy to follow
Sep 19, 2018 Everything works with provided data and the scale is good for use in class Could you provide the fragment size separating the paired ends? It would also be nice to have more info for instructors about the genome for doing additional exercises based on the assemblies.
21 responses
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Nov 20, 2022 Everything, except the Velvet choice. Use another software besides Velvet, since it's deprecated and it's not working.
Jun 30, 2022 most of the functionsare different what is given here please insert screen shorts of the results, how the output look like
Apr 26, 2022 It is easy to follow up as you practice. More examples to practice with.
Mar 12, 2022 Simplicity. Considering this is an introduction to assembly, it would be helpful if the steps are complete as some steps may have been skipped. It would also be useful if pictures can be added for some steps. When ran, the results stated in this tutorial doesnt match with the output even if the instructions is strictly followed
Oct 26, 2021 Clarity, granularity, hands-on Could have a similar tutorial for long read assembly (Nanopore, PB) , and I suppose 'hybrid assembly' , but this one is probably adequate for all these purposes.
Feb 10, 2021 you may show the progression files in green to show us the file we have after each step i have problem with FASTQ interlacer i follow the tutorials and after this step i have two files one of them is empty and it's not working for the further stem with velveth so i'm stock at this step i don'understand why
Oct 9, 2020 Easy to follow The options that appear now, are not the same that this tutorial shows.
Jul 2, 2020 Simple enough. There isn't much information to give the learner the background to interpret their own data. There should be an introduction of what each of the parameters specified for the hands-on session means and why the learner should be setting them as instructed. That's the only way to know whether this tutorial is suitable for the learner's own dataset to follow.
Jun 9, 2020 The pace and the content covered are great!!!
Apr 18, 2020 the hands on exercises There was no Icarus viewer
Oct 21, 2019 Step by Step instructions Feeding in multiple samples at the same time for FastQC
Jun 3, 2019 the real data analysis provide links to the tool side by side
8 responses
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Jan 15, 2021 the explanations are well
Apr 16, 2019 easy to follow, step by step
1 responses
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Apr 1, 2020 I miss some screenshot of how my data should look. At one point, in one of the steps where I had to choose some columns from a matrix to work on, I kept getting a wrong result. And I think the reason was, that I had something different in some of the columns than what I should have (so if for example I was asked to choose column 1, the data I was trying to get was actually in column 2) - if there were some screenshots of what the data should look like, I might have been able to see if I had a column too much
7 responses
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Aug 13, 2021 The activity was very interactive with a good combination of theory and practical The last step on NCBI BLAST search was not clear enough to a biginner like me
May 18, 2021 The basics of each step explained very clearly. Maybe the names of the files which need to be put in the field for the tool. Took a bit of time to understand in few places.
Feb 19, 2021 How in depth and clear it was.
Feb 19, 2021 it was very helpful.
Jan 19, 2021 Très didactique Peut être ajouter des copies d'écrans de l'historique ? (repérer les numéro d'actions) Mais peut être "anxiogène" si on a refait certaines opérations et que l'on perd ce repère de numéro...Donc non en fait :)
Jul 28, 2020 It was very detailed and easy to follow
Apr 22, 2020 The format and outlining are fantastic Add a screen shot or graphic to illustrate the major steps in this workflow
21 responses
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Date What did you like? What could be improved?
Mar 31, 2022 pictures - screenshots can be added
Mar 22, 2022 I learnt new tools that i haven't used before
Mar 17, 2022 i liked on how to polish nano-pore reads
Mar 15, 2022 Very easy to use and effective
Mar 15, 2022 good intro course on assembly some more theory about polishing and why
Mar 15, 2022 All aspect Not much improvement
Dec 23, 2021 Circos plot of the data should also be included.
Nov 30, 2021 Very assertive and good guidance More intuitive guidance
Jul 10, 2021 The overall training session was really nice. However, some more information regarding the viewing in Jbrowse should be discussed like what to analyse in Jbrowse, how to spot irregularities and how to spot meaningful data? What kind of useful data can be visualized or can we get from the visualization in the Jbrowse.
Jun 30, 2021 The idea of comparing long and short reads and how to use short reads to polish the results It would be great if there was a little explanation of how the tools work
Feb 20, 2021 I´d like to know how I can get a unique assemble using more than one pair of Illumina reads for the same DNA, for example the same bacterial strain. It is possible?
Feb 16, 2021 Loved the self training with new data at the end. Helps user create a workflow to re run the steps rapidly and compare results. The tutorials were very clear and easy to understand
Feb 15, 2021 Clear and easy
Jan 2, 2021 Clear Explanations I noticed the "Note: this tool is heuristic; your results may differ slightly from the results here, and if repeated." But mine only showed one contig, with a length of 158kbp. I would consider this very different, not slightly different. Maybe add a few more examples of "slightly different" results I am running the tool again to see what I get. Additionally it took a long time to run this tool; almost an hour. So it would be nice to know approximately how long a tool is going to take, (given the fastq file & runtime parameters), or maybe show the log file while it is running (assuming the actual tool writes to the log file rather than just storing the info in memory and writing the log at the end...)
3 responses
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Jul 8, 2021 the lessons not sure
1 responses
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Feb 21, 2022 A clean flowchart of methods with an explanation for the purpose of each step. As a case study, a bad genome assembly or an assembly with incorrect parameters in various steps could be shown
2 responses
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Sep 1, 2022 To test the tools of assembly in a control dataset I think it could be valable to understand the tools and the parameters of the tools while using them: to not do it without thinking it through. I think it is better to understand to remember.
Jun 8, 2022 straightforward would have liked to have some practice viewing the assembly graphs and with visual methods for comparing genomes (e.g. dot, synteny plots)
2 responses
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Oct 25, 2022 Table to gff3 tool does not exist anymore. When I use the tutorial mode on galaxy and click on the table to gff3 hyperlink button, i get this message: Loading tool toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2 failed: Could not find tool with id 'toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2'. Do you have any advice on which other tool to use? Also, in a prior feedback I mentioned that I could not find select the lines, but it is actually there I found it in the end. sorry for the mistake.
Oct 25, 2022 It was easy to follow the steps and the functions ran in a good amount of time (relatively fast) - I got stuck in staramr. there was a recurrent error due to ERROR: 'Predicted Phenotype'. This error was reported. it appears to be due to a problem of compatibility with the pandas version (https://github.com/phac-nml/staramr/issues/115) - Genome annotation using Prokka, step 2 (Select lines that match an expression) has changed names to Search in Textfiles (grep) - Table to GFF3 function: I was unable to find this function under the Galaxy tools. downstream commands could not be ran.

Climate

7 responses
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3 responses
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Oct 14, 2021 Very nice intro. Learned about the difference between climate and weather!
Oct 8, 2021 Clear introduction in using galaxy to explore/map climate data. More detailed explanation of the inputs @map plot gridded (lat/lon) netCDF data. Did not understand the R as input “variable name as given in the netCDF file”. For other Essential Climate Variables I guess Ill have to change that input?
Jul 19, 2020 Exposure to climate concepts and tool choices.
1 responses
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May 5, 2021 Sometimes it is hard to find a specific thing that we need to click on when we don't know where it is located on the screen.
1 responses
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1 responses
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1 responses
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Computational chemistry

25 responses
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3 responses
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Jul 31, 2021 AWWWWWWWWWWWWSOME
Sep 26, 2020 Its a neat tutorial. There is no source code for me to follow along. I pulled the autodock vina docker image down and am trying to learn how to use it and this did not give me any commands to execute in the docker container. Everything is coupled to this galaxy software and I just need source code.
Nov 11, 2019 The whole process of creating molecules A video or two illustrating the end goal
2 responses
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Nov 18, 2019 The feeling of creating something on my own Nothing
6 responses
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Oct 31, 2022 method present and images
Jun 8, 2022 The explanation of every step which provide understanding even to beginners. The different methods used in different steps of simulation should be explain in a such a way that the person can understand which method he should apply to his experiment.
Feb 26, 2022 Easy to follow and execute. The order of selecting parameters can be sequential as it appears on the galaxy platform
Dec 7, 2021 Easy to follow, good reasoning for each step, mostly successful results For some reason, I can't get this to work with NMR-derived pdb files
Jan 11, 2020 Interpretation of the results and being easy to follow Adding more explanation on how to visualize the trajectory, completing the analysis, also showing how to perform this run with a ligand also will be highly appreciated.
3 responses
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Feb 26, 2022 The further analysis links seems to be broken/unavailable: https://github.com/galaxyproject/training-material/tree/main/topics/computational-chemistry/tutorials/analysis-md-simulations/workflows/advanced_workflow.ga
Oct 28, 2021 yes yes
May 21, 2020 Analysis of Rg, Hydrogen bonds can also be explained
9 responses
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Aug 14, 2022 merge gromacs topologies doesn't exist in https://cheminformatics.usegalaxy.eu It was not possible to complete the tutorial without this tool
Mar 30, 2022 Great tutorial for intoducing the computational chemistry
Mar 29, 2022 optimization everything is perfect!
Mar 16, 2022 Very simple to understand easy to do Nothing, it is very complete
Jul 15, 2021 Easy to go through and explanations help to understand the results better. Too many abbreviations
Feb 28, 2021 Explanations and step by by procedure explained
2 responses
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Contributing to the Galaxy Training Material

21 responses
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5 responses
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Oct 23, 2021 I have got the following error. The tutorial did not work for me. training-material$ make serve find: ‘_site/training-material’: No such file or directory find: ‘_site/training-material/*/*/slides/*’: No such file or directory find: ‘_site/training-material’: No such file or directory Tip: Want faster builds? Use 'serve-quick' in place of 'serve'. Tip: to serve in incremental mode (faster rebuilds), use the command: make serve FLAGS=--incremental mv: cannot stat 'Gemfile': No such file or directory mv: cannot stat 'Gemfile.lock': No such file or directory Configuration file: /home/alice/scchoi/downloads/training-material/_config.yml Dependency Error: Yikes! It looks like you don't have /home/alice/scchoi/downloads/training-material/_plugins/jekyll-environment_variables.rb or one of its dependencies installed. In order to use Jekyll as currently configured, you'll need to install this gem. If you've run Jekyll with `bundle exec`, ensure that you have included the /home/alice/scchoi/downloads/training-material/_plugins/jekyll-environment_variables.rb gem in your Gemfile as well. The full error message from Ruby is: 'cannot load such file -- bibtex' If you run into trouble, you can find helpful resources at https://jekyllrb.com/help/! ------------------------------------------------ Jekyll 4.2.1 Please append `--trace` to the `serve` command for any additional information or backtrace. ----------------------------
May 19, 2021 Everything :) topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.md is no longer found, example can be changed to "topics/introduction/tutorials/r-basics/r_introduction.md" instead
Jun 19, 2019 Clearly explained. In the first step (install requirements) - does there need to be an extra step before step 5, that says "conda activate galaxy_training_material" ?
Feb 8, 2019 Clear wording. As a Windows user, I was not able to install requirements successfully.
Oct 22, 2018 Very very straightforward ! Nothing...
1 responses
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Feb 16, 2019 the option to automatically extract all steps of my workflow instead of typing them all is sooooo increadibly helpful!!!
1 responses
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6 responses
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May 19, 2021 That it is a step by step <3 The master branch on my side is called main
Oct 21, 2020 Very clear directions - thank you! The key points at the end are a great concise summary.
Apr 20, 2020 Liked the clean explanation with visuals. Great Job. In clears the process flow for beginners. 1) In situations where I'm working on a feature "F1" in branch "B1", while I prepare to make a PR, do I need to keep my local up-to date with Upstream before PR? 2) After deciding my feature branch is good to go for PR, can I checkout to Master and pull my feature first? What's the process for updating my Master with my new feature I developed? Please answer this. I always have this confusion. Thanks.
Apr 19, 2020 The presentation was very clear
Aug 30, 2019 Every thing was great especially the graphics. Thanks for all the help!! Every thing is fine and up to date though I am not an expert!
Aug 26, 2019 It's easy to understand More diagrams
3 responses
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Feb 11, 2020 the "Testing the workflow" part I had to deal with "fetch_url_whitelist" option, as my input file was located on my galaxy server.
Feb 11, 2020 the "Testing the workflow" part I had to deal with "fetch_url_whitelist" option, as my input file was located on my galaxy server.
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Oct 12, 2021 Very detailed It would help if the sites name and the drop-down button at the top is static. So even when I scroll to to end of this page, I can easily click on the drop-down button and access other files without having to scroll all the way back up
Jul 8, 2021 Very complete, sufficiently detailed to allow non-computer-science people to go through this with all the questions we could have being answered. The video from GCC2021 training week corresponding to this topic is also very well. Maybe a link to this video for people who need to see things in movement to be reassured would be nice :)
2 responses
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Mar 28, 2022 The directions on how to create a pull request i think a video could me made.
Oct 11, 2021 The tutorial is so detailed that even a preschooler would get it by simply following the steps! I found it so useful, I'm going to make my first contribution right away! I'd suggest each of the topics under the "objectives" in the overview box be made clickable, so each topic can be reached right from the top without having to scroll all the way down the page.

Development in Galaxy

4 responses
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4 responses
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Mar 15, 2022 Explanations on how to create a galaxy tool Put planemo install first
Mar 15, 2022 clear for a beginner maybe planemo could be the first step, because needed in the wrapper section
Feb 21, 2022 As usal, the step by step procedures. It is not clear that we have to set up the test-data folder and collect the bam files by our own for passing the test in the planemo section.
Jul 1, 2021 Plenty of detail, teaching by example, and context provided > Written in markdown ### General - Should I be working in a clone of `galaxyproject/galaxy`? - Where are all the galaxy tools? They don't seem to be in the galaxy/tools/ dir? This is covered well in the "contributing" video at the end but could have mentioned briefly at the start. More generally, it would be good to explain that `galaxy-core` has built-in tools (with no `.shed.yml` file) and that all contributed tools (like we're building) are installed from an available toolshed. - I'm not sure if I should actually be following along with all of this... should I actually make a PR for a new Bioconda package in a tutorial? It would be great to clarify what the participant should be doing NOW versus what they would do in a genuine tool wrap. Also, presumably the package sometimes exists already in Bioconda? (I used an existing conda package in my 'practice' tool wrap). - At the end of the "Toolshed file" section: "In the case where the directory represents a group of tools or a ‘suite’, there are additional overarching sections into which the above tags fall" ... seems to imply that parent dirs can/should have a `.shed.yml` file too? Or is it only in `suite` and `suite/tool` dirs? Would be great to clarify or provide a link to a toolshed on GitHub as an example. - "Macros" section: should note that whitespace inside `<token>` tags matters, and it will not be trimmed by the XML parser! (Should be picked up by the `planemo lint`) ### Typos - `bellerophon.xml` typo under "discover datasets": `directory="outputs"/>>` - And "Outputs section" (should have closing `/>` on `<data>` according to planemo): `<data name="outfile" label="${tool.name} on ${on_string}" format="bam">` - "crate an ad-hoc Galaxy" ### Planemo - Didn't work when `pip` installed into `conda` env (dependancy errors). `pip` install into a `virtualenv` env worked. - `pip` installing `planemo` into virtualenv requires `apt install python3-venv` as a dependancy **Some small issues with Planemo** - `tool_test_output.html` output is a bit weird to navigate - buttons don't look like buttons (no hover effect) so most of the content is hidden until you realise there are clickable elements - `planemo serve` doesn't print the local address at the end of output (had to scroll up a few pages to find `http://127.0.0.1:9090`)

Ecology

7 responses
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3 responses
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1 responses
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2 responses
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Jan 20, 2021 Very clear Where to find the tools (not always easy in the toolbar)
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Apr 14, 2021 I liked that it is possible to use real data and explore multiple tools. It was relatively easy to follow all the way to the final step. I could also take the Structure output and run it through Structure in Galaxy or in my own PC to further demonstrate that the SNP data can be analysed with population genomic software. Some of the instructions need to be updated to the latest versions of the tools available in Galaxy. I could not tell which population (1 or 2) was the freshwater and which one was the oceanic, so I assumed 1=freshwater, 2=oceanic. It would also be good to see some of the "expected" results, just to verify that what has been done is working fine and that students are on the right track.

Epigenetics

46 responses
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6 responses
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Feb 1, 2021 Covered all the steps Parameters could have been explained
Jul 19, 2020 step wise explanation was very clear comparison of two HiC datasets
Dec 9, 2019 Note from @jennaj: Noticed mismatched tools across tuto components. The "Reads mapping" step description states "We have used the HiCExplorer successfully with bwa, bowtie2 and hisat2. In this tutorial we will be using Map with BWA-MEM tool." *However* the "Hands-on: Mapping reads" box has the mapping tool specified as "Map with Bowtie". The tool name doesn't fully match a Galaxy wrapped tool but looks as if it was intended to match "Map with Bowtie for Illumina" tool from some earlier tutorial revision, but the tool options/settings are actually for "Bowtie2" (tweak SAM/BAM output). The tuto workflow uses "Map with BWA-MEM (Galaxy Version 0.8.0)" which isn't available at EU or ORG (or that version is hidden in the tool panel + tool versions menu). --------- Punchline ... three different tools are mixed up, at the first step of the tuto after loading the initial fastq inputs. Probably should adjust to make all for either Bowtie2 or BWA-MEM using a version available at EU (so it can be run there). Be nice to have this work at (at least) one of the usegalaxy.* servers :) ORG doesn't include HiC tools. Will ticket this and whatever else is found after reviewing the remainder of steps.
Feb 28, 2019 Nothing bad, just I do not have sufficient background knowledge to comprehend everything. Nevertheless, very well-structured for a beginner to learn.
Sep 18, 2018 perfect step by step !!!! maybe use human data ??
9 responses
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Jun 9, 2022 nothing everything
Jan 13, 2022 Data set can not be found
Nov 17, 2021 The programs were not available at Galaxy
Sep 20, 2021 It would be great if this can be updated based on the newest version of the packages used in the tutorial. Some of the parameters cannot be set as shown in this tutorial or should be set in a different way.
Sep 8, 2021 Instructions about finding tutorial data in a Data Library need to be updated. In this tutorial and probably others. Tutorial data is now nested at usegalaxy.* servers -- and that change is confusing some learners. I've been telling people to search data libraries with the keyword "GTN" then to navigate down through the topic to the specific tutorial. Not all public servers will host the data in Data Libs, so even that advice needs a tune up to be consistent/accurate across tutorials. (@jennaj)
Mar 24, 2020 The degree of detail. I loved that even the parameters for the different tools were explained. I don't know if this is comparable to a real experiment analysis, but it surely felt as that. Congrats! The Genrich tool is only available at the GalaxyEurope server. It would be nice that a warning would be given at the beginning of the tutorial, so that the whole analysis could be done there and avoid migrating data between Galaxy servers.
Feb 4, 2020 The tutorial is self explanatory and very easy to follow for individual hands on
Sep 26, 2019 The good explanations during hands-on training Maybe too different analysis for one day (HiC and epigentics), maybe a longer session for each would help understanding
8 responses
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Jun 13, 2022 it was clear maybe you could explain the file formats and what the tools do in a more clean way
Dec 16, 2021 Well detailed method of ChIPseq and associated explanations The title in itself doesn't really reflect the final results of the tutorial, with the data used one do not really identify TAD on the inactive X chromosome...
Jan 10, 2020 In step 6 it is explained to insert each of the datasets one after the other (with Concatenate datasets tail-to-head). However, one can insert more than one dataset at once with this tool, so why not do that? Also, it should read "Redo for the remaining four outputs of MACS2 callpeak" - it is six in total and in the first step you concatenate two and then add the remaining. Why are the bedgraph files created if they are not used for anything?
20 responses
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Mar 22, 2022 The fact that there are explanations for all steps. All were perfect!!!
Jun 18, 2021 Everything was explained in detail, easy to follow
May 10, 2021 The depth of the tutorial, the examples of bad quality data, the explanation why these tools are used and sometimes alternatives, and the overview figure in the conclusion.
Apr 21, 2021 Easy to follow
Oct 15, 2020 Everything it is good overall
May 29, 2020 Detailed explanation of each step Comparison of two ATAC-Seq datasets
May 28, 2020 Quite easy to follow Bit more interpretation of output
Apr 12, 2020 Entire organization, rationale for the steps taken link to smaple out put or all steps like EMBOSS tutorial does
Mar 24, 2020 The degree of detail. I loved that even the parameters for the different tools were explained. I don't know if this is comparable to a real experiment analysis, but it surely felt as that. Congrats! The Genrich tool is only available at the GalaxyEurope server. It would be nice that a warning would be given at the beginning of the tutorial, so that the whole analysis could be done there and avoid migrating data between Galaxy servers.
Mar 10, 2020 I have to say the full workflow is very useful for the people who did't know this for a long time, thank you so much. but the tool 'Genrich',I did't find it on the Galaxy... I can't find some tools in Galaxy,
Feb 26, 2020 so great!!! its so helpful!!!!! nothing.
Feb 25, 2020 The easiness and the clarity of the examples provided. A print version of the tutorial or pdf to save for offline use.
Dec 12, 2019 a good resource for a training session too many steps where you have to 'prepare' data, e.g. sorting the provided bed file
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Jul 1, 2021 update is required

Foundations of Data Science

23 responses
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15 responses
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Nov 9, 2022 Flow of information Add videos and demonstrations
Sep 9, 2021 none of the essentials is working gx_put(), gx_get(), and gx_save() none of the essentials is working gx_put(), gx_get(), and gx_save()
Mar 28, 2021 Simple languange, hands-on example and exercises with answers hidden. I know it is a lot to ask, but adding matrices would be helpful
Feb 17, 2021 I like the examples,being related to genomics . I am not sure if I would grasp it without previous knowledge.
Feb 15, 2021 Very helpful basics of R
Sep 19, 2020 The hands on explanations Couple of sections where the description is a little vague
Aug 2, 2020 Good with exercises > snp_chromosomes_2 <- as.numeric(snp_chromosomes_2) Warning message: NAs introduced by coercion In the above code, I think need to correct object name from snp_chromoosome_2 to chromosme_2 (we assigned this name)
Jun 30, 2020 Good guide, with usefull examples
Jun 7, 2020 Thank you so much for providing the related material for R
Apr 3, 2020 It was easy to follow
Feb 12, 2020 The instructions were clear and neat. Also, it covers important aspects of the language. There should be one task that push us to combine and use the learned knowledge.
6 responses
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Feb 15, 2021 Very interesting libraries (tidyr and dplyr) for data analysis More self training exercise
Dec 3, 2020 so easy and clear
Jul 3, 2020 Easy to follow and very usefull examples
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Galaxy Server administration

157 responses
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19 responses
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Mar 18, 2022 The straightforward pedagogical approach I think it is perfect as is
Mar 15, 2022 For me it is not clear wether the apikey example use of vaults is the best. Might it be better to set an example about ssh passwords to connect remote servers?
Nov 4, 2021 Really clearly written and well explained, including details that can go wrong or be confusing (the cowsay bit gave me a chuckle). Not overwhelming, unlike some other tutorials I tried.
Feb 1, 2021 It gave an excellent crash course in Ansible and how best to use it in Galaxy Possibly one or two links to other Ansible resources in the docco, but can't think of anything else.
Jan 25, 2021 The incremental approach to a rather complex system I was confused at first by the "service" service. More real, less abstract examples would be clearer, IMO
Jan 25, 2021 specifiying that all commands (including andible-galaxy) should be rin in the `intro` directory, I had to rsync my new `~/roles` folder to intro
Jan 25, 2021 It is easy to follow
Jan 25, 2021 Clear examples More information on using git repos with ansible would be helpful
Jul 17, 2020 This is something new. I enjoyed it.
Mar 2, 2020 All of it Looks very good, with basic sample tasks.
Feb 14, 2020 Step-by-Step guide, simple and well informative
Jul 1, 2019 Examples and documentation are easy to follow
Nov 15, 2018 TEST TEST
Nov 2, 2018 excellent intro, thanks!
Oct 30, 2018 It's easy to follow. For clean Ubuntu 18.04 Ansible couldn't find python (it was not installed, weird), so it crashed. There should be rule added to check and install python if it is not installed. Refer to this solution - https://gist.github.com/gwillem/4ba393dceb55e5ae276a87300f6b8e6f.
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Jun 24, 2021 realistc examples More details regarding used scripts and templates
Jun 20, 2020 Basically I love all of them, It's simple, clear and easy to follow. Would be nice to have more complex examples to follow, if that possible
Dec 19, 2018 Really detailed, could use it for my project for creating my project maybe go deeper and show a template for a project
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Mar 17, 2022 I would be great if it could explain how to run ephemeris from a different machine (for example my local machine) but deploying galaxy on the vm
Mar 14, 2022 The slides gave a really useful overview of toolsheds and how to configure them. It would be useful if the links to ephemeris commands would open in a new tab (I would prefer this for links in general but especially in this case as you have to do it in the middle of a task and it's not just further reading)
Jun 29, 2021 The practical approach
Jan 27, 2021 easy to understand and follow
Jan 26, 2021 It shows me a really easy way of installing tools from tool shed avoiding the use of the graphical interface. That is perfect when you need to install many tools at once. It could be explained how to include this tasks in the ansible playbook (if possible) in the case of a full re-installation of Galaxy. Or maybe better separate the two steps...
Jan 26, 2021 all the examples worked The flow of the tutorial feels awkward in places - you extract the workflow but then install a tool singly before going back to the extracted .yml to do a batch. Not directly related to this tutorial but coming from the previous Galaxy setup tutorials, I'm left thinking - what happened to Ansible and the concept of reinstalling the entire Galaxy in one playbook?
Jan 26, 2021 very beneficial pace!
Jan 26, 2021 Everything, from top to bottom.
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Aug 30, 2022 The instructions were clear and helpful (especially with the video alongside) It would be super helpful if there were more subsection links! I set followed this tutorial to setup a server for my team, and when they had questions or wanted more info on why or how I did certain things it would have been nice to be able to link them more specifically to the step I wanted instead of the bigger section and then giving them key words to search for
Jul 28, 2022 relatively easy to follow, concept explanations are great
Jun 29, 2022 tree -l 2 was helpful as otherwise unclear which file goes where Current version of the tutorial is broken, consider rolling back to archive. Ansible errors very hard to troubleshoot - ideally add more tips where things can go wrong, for ex ansible vault seems to enter an unfixable state if you mess up the secret yml file and have to make it again
Mar 18, 2022 how seamless it was to deploy it
Mar 16, 2022 Clear and structured - everything ran without issues on my machines
Mar 16, 2022 the structure, it was very well organized
Feb 15, 2022 Pretty simple step-by-step; A couple of syntax errors are included to make things "interesting" when trying to deploy. Found another syntax error in the referenced tutorial: In the galaxy.j2 file, "location /_x_accel_redirect" should be "location /_x_accel_redirect/"
Jan 15, 2022 Code examples that you customize to your server set-up; hints and sidebars are very helpful; as is the in-depth explanation of what the code is doing. One solution to errors that arise would be to try newer playbook versions. Although the tutorial cautioned that newer versions could create problems - in my case it solved problems. I found that the version of galaxyproject.galaxy used in the tutorial-- version: 0.9.16 was incompatible with Ubuntu 20.04 LTS - resulting in a failure to install "futures". When I changed to the newest galaxyproject.galaxy version the problem was solved.
Sep 14, 2021 I think there is an error in the instructions around which galaxy release to use. https://training.galaxyproject.org/archive/2021-08-01/topics/admin/tutorials/ansible-galaxy/tutorial.html#galaxy step 9. Fails with a pip install error for attmap at galaxy dependency installation: FAILED! => {"changed": false, "cmd": ["/srv/galaxy/venv/bin/pip3", "install", "--index-url", "https://wheels.galaxyproject.org/simple/", "--extra-index-url", "https://pypi.python.org/simple", "-r", "/srv/galaxy/server/lib/galaxy/dependencies/pinned-requirements.txt"], "msg": "stdout: Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple\nIgnoring importlib-metadata: markers 'python_version < \"3.8\"' don't match your environment\nIgnoring importlib-resources: markers 'python_version < \"3.7\"' don't match your environment\nIgnoring pathlib2: markers 'python_version < \"3.6\"' don't match your environment\nIgnoring ruamel.yaml.clib: markers 'platform_python_implementation == \"CPython\" and python_version < \"3.8\"' don't match your environment\nIgnoring typing: markers 'python_version < \"3.5\"' don't match your environment\nIgnoring zipp: markers 'python_version < \"3.8\"' don't match your environment\nCollecting adal==1.2.4\n Using cached adal-1.2.4-py2.py3-none-any.whl (55 kB)\nCollecting amqp==2.6.0\n Using cached amqp-2.6.0-py2.py3-none-any.whl (47 kB)\nCollecting appdirs==1.4.4\n Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)\nCollecting attmap==0.12.11\n Using cached attmap-0.12.11.tar.gz (9.9 kB)\n\n:stderr: ERROR: Command errored out with exit status 1:\n command: /srv/galaxy/venv/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '\"'\"'/tmp/pip-install-rswp62oy/attmap_d1e6f1f187954e539109df4d7760fde7/setup.py'\"'\"'; __file__='\"'\"'/tmp/pip-install-rswp62oy/attmap_d1e6f1f187954e539109df4d7760fde7/setup.py'\"'\"';f = getattr(tokenize, '\"'\"'open'\"'\"', open)(__file__) if os.path.exists(__file__) else io.StringIO('\"'\"'from setuptools import setup; setup()'\"'\"');code = f.read().replace('\"'\"'\\r\\n'\"'\"', '\"'\"'\\n'\"'\"');f.close();exec(compile(code, __file__, '\"'\"'exec'\"'\"'))' egg_info --egg-base /tmp/pip-pip-egg-info-2gc_ov_9\n cwd: /tmp/pip-install-rswp62oy/attmap_d1e6f1f187954e539109df4d7760fde7/\n Complete output (1 lines):\n error in attmap setup command: use_2to3 is invalid.\n ----------------------------------------\nWARNING: Discarding https://files.pythonhosted.org/packages/d0/d4/8b8fca155270a6675bac9a1e49b7c616ae763f66af7b836042ecfc805552/attmap-0.12.11.tar.gz#sha256=95b1f7dbcdad7278a3702fa921be6271046c96e1c9ed9feb10e0d4c13092b0a0 (from https://pypi.org/simple/attmap/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.\nERROR: Could not find a version that satisfies the requirement attmap==0.12.11 (from versions: 0.1, 0.1.1, 0.1.2, 0.1.4, 0.1.5, 0.1.6, 0.1.7, 0.1.8, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.10, 0.11, 0.12, 0.12.1, 0.12.2, 0.12.3, 0.12.4, 0.12.5, 0.12.6, 0.12.7, 0.12.8, 0.12.9, 0.12.10, 0.12.11, 0.13.0)\nERROR: No matching distribution found for attmap==0.12.11\n"} This occurs with galaxy_commit_id: release_20.09 (as per the instructions), but changing to release_21.05 makes the error go away.
Jul 1, 2021 Simple and short and easy THX
Jun 28, 2021 All points were very well explained
Feb 1, 2021 Some good things to note and keep track of regarding moving to production, especially updating the version.
Feb 1, 2021 Realy clear and solid explanations of how to use Ansible for Galaxy installation
Jan 27, 2021 The clear explanation of every part of the roles, modules etc. What they do why they're there. Even if I wasn't interested in everything it's good to know that if I ever need that information I can look back to this tutorial I don't know if it can be improved but the actual time of the tutorial is really long. After watching it, I totally understand why but if it could be something like 1 hour videos (or less) that would be less tiring. Of course I am fully aware that there is a broad range of topics that need to be covered.
Jan 27, 2021 the step by step exercises for me as a noob some diagrams or schemes would often be helpful to see how things relate to each others
Jan 25, 2021 very easy to follow; excellent documentation note about using non- let's encrypt certificate
Jan 25, 2021 very structured and understandable templates/nginx/galaxy.j2 -> "uwsgi_pass 127.0.0.1:8080" should not be configured statically and changed to a variable from the groups_vars if the port is changed there in the uwsgi variable settings
Aug 10, 2020 It is very practical tutorial I had to change those two variables to make it work on my ubuntu machine: "virtualenv_command: pyvenv" as it also recommends in README but not the default in the galaxy role "__galaxy_mutable_config_dir: "{{ galaxy_root }}/var/config" " my Ansible didn't understand the previous line defined variable, so I had to define "__galaxy_mutable_config_dir" base on "galaxy_root" variable
Jul 7, 2020 In the nginx-part, the template needs an update to reflect 20.05 changes. The folder /blue doesnt exist anymore, its just "alias {{ galaxy_server_dir }}/static/style" # The style directory is in a slightly different location location /static/style { alias {{ galaxy_server_dir }}/static/style/blue; expires 24h; }
Jul 6, 2020 In the section "Galaxy" we add uchida.miniconda which has to run as galaxy user and a few linse above is explained that a new user is created without sudo privileges for security reasons. The execution of uchida.miniconda with become: true and become_user: galaxy will fail, because this role requires sudo. I tried to install the dependencies tar and bzip2 in my playbook beforehand, but the role still requires sudo to check if the packages are installed. When i install the package with a root-user, it is possible to execute the /tmp/Miniconda...sh file with the galaxy user. Not sure if other stuff works in miniconda too. Why does this role need to be executed as galaxy user? This is somewhat unclear and leads to an installation-error.
May 8, 2020 The difference between galaxy_server_dir and galaxy_root is unclear. Should they be nested? Which of these is needed in a shared file-system? Maybe provide best-practice values for both, so it becomes more clear how they interact with each other.
May 5, 2020 Tutorial includes code steps very clearly. This is focused for paid distros. Centos 7/8 builds do not work due to package requirements and availability
Mar 2, 2020 Following the tutorial is pretty straightforward It would be interesting to have a big picture of the processes / config files. Literally a big picture about which parts are we configuring and what are the implications.
Mar 2, 2020 exhaustive it would be nice to go a bit slower during the Galaxy installation, it was quite quick !
Feb 14, 2020 Everthing
Jul 1, 2019 extremely well done - thank you training material authors and presenters 1) ssh connection timeout is too short, disconnects while running playbooks. (2) sometimes the insertion point for yaml section in the exercices could be more explicit
Jul 1, 2019 I already followed this tutorial by my own before GCC. I would add all the galaxy.yml and modify it instead of copy/paste some element in the playbook. For me, it's easier to get update shiped with each Galaxy update.
Jul 1, 2019 Very good step by step procedure. perhaps more emphasis on some steps (geerlingguy.pip during supervisord)
Jul 1, 2019 well explained :) sometimes it is not clear in the exercises which files have to be edited, or the code is not ready to copy-paste, which leads to misunderstandings. I would love to see the whole explanation of the variables of the config files you did (specially nginx) written down to check them when needed.
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Mar 18, 2022 Very clear! It's simple and very important to know
Mar 17, 2022 the pace, simon explains everything really well and understandable
Mar 15, 2022 Clear explanation of what CVMFS is for and how it works
Jun 29, 2021 Very clear explanation
Jan 28, 2021 CVMFS is a great addition both for Galaxy and in general. It was a great thing to know. In the tutorial nothing. It's perfect. I would like CVMFS to include reference genomes indexed for methylation analysis (e.g. with Bismark). I dropped a question about it in slack as well.
Jan 27, 2021 very easy to follow and understand.
Jan 27, 2021 This is really cool!!!! For the most used datasets (for ex. hg38) could we have a local copy, or would that be irrelevant? Could you explain how to calculate a good cache space? If I use a cluster, will I need to configure this FS in each node (given that the folder is at / directly)?
Jan 26, 2021 Clear, straightforward, brief and complete
Jan 26, 2021 You guys rock! this CVMFS thing is so coool!
Jul 4, 2019 the samples are great and its great to have the copy capacity, but some of those copies could mess people up (ones with ..., snippets of yaml that start with ---, etc)
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Jul 3, 2019 this was way super cool maybe specify that the parts in Setting admin... part 1 should go under the galaxy: heading for those not as familiar with galaxy configs? or can we assume they're all savvy? templates/deployment_web.yaml -> dash, not underscore
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Jul 1, 2021 Very clear, even though the material is complex
Jan 28, 2021 This is a very well written tutorial. I really appreciated how we were shown ways to thoroughly check that rabbitmq was working as expected before moving on to the next step.
Jan 28, 2021 Good detail The tutorial assumes a bit more knowledge than a lot of the others so it won't be as useful for someone who comes to it stand-alone as a pulsar via ansible setup guide
Jan 28, 2021 This is amazing!
Mar 4, 2020 Content Maybe still take it slow when editing the various files. It's sometimes hard to follow with the numerous kind of configuration files.
Mar 4, 2020 Very comprehensive tutorial. Helped me a lot
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Feb 5, 2021 The simplicity Add a short section on using nginx basic authentication to secure it from public eyes
Jan 29, 2021 quick and easy Link to guide on how to secure it
Mar 4, 2020 Thanks to ansible, easy to install :)
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Jul 1, 2021 The installation part was very clear and good to follow The Grafana part was difficult to follow because the version of the tutorial was different from the installed one
Jan 29, 2021 Ansible instructions worked I found the content on Grafana and monitoring/alerts really confusing, it felt almost like it is for an older version of Grafana.
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Mar 18, 2022 Very simple and clear
Jun 29, 2021 Very interesting, the step by step approach is very clear
Jan 27, 2021 all of it! maybe some notes about what may require proxies
Jan 26, 2021 Great clarity. Thorough tutorial, leaves no stones unturned Modify the file parts (e.g. points 1. and 5. of "Hands-on: Configure Galaxy to use Singularity") are clear and a useful exercise to better understand the ansible and galaxy hierarchy, but if for some reason you made a mistake in a previous step, it could be useful to also have a snippet of the whole modified code to fasten the correction process and avoid backtracking.
Jan 26, 2021 Nice, easy to follow I'm coming at this as a non-galaxy user so jumping straight into the interface was initially a bit confusing, a quick video tour of the Galaxy interface (~5 minutes) beforehand would have made this easier for me
Jan 26, 2021 Everything is great. sysadmin part could be little bit slower, its hard to catch on for us who are not from purely IT background.
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Jul 12, 2021 very clear and straightforward.
Jun 29, 2021 Very clear step by step
Jan 29, 2021 There is a big chunk of the tutorial misssing from the video (the video is stuck in the setup stage).
Jan 27, 2021 very helpful some video issue around 8m
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Jun 30, 2021 Very clear explanations
Jan 27, 2021 I really need this knowledge. I have stuck in the part of editing templates/galaxy/config/job_conf.xml.j2 because some lines differ from the resulting file from previous session (namely singularity was set as default) and I had to compare the file showed in the video with the file I had. I took some time, but it worked at the end. It seems not so complicated now, but it will be when connecting to a living cluster. What happens when I have SLURM already configured at the server? And MUNGE (this guy made some nodes crash here because of very large log files), do I need to configure it in the cluster? It was not clear.
Jan 27, 2021 fantastic, incredibly helpful. trainer is really great. Would like info on adding to existing clusters (ie., SGE, etc)
Jan 27, 2021 Just the right amount of content, Slurm is so large it would have been easy to get over complicated Minor: the references to pulsar in the examples could be confusing, might be worth adding a warning for anyone who is going through this tutorial before the pulsar tutorial
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Mar 17, 2022 The existence of the dynamic job destinations
Jul 22, 2021 Lots of detail and a selection of realistic examples The directories "./templates/galaxy/dynamic_job_rules/" and "./templates/galaxy/tools/" should actually be under another directory "./files/galaxy/ ... " for the latest Ansible roles to work!
Jun 30, 2021 Great introduction and very useful starting point for beginning to apply these features
Jan 28, 2021 This is a powerful way of controlling the resource usage according to tool requirements. This task includes many layers of complexity. It would be nice if, at the beginning or ending of each subtopic the needed changes were pointed in the file tree. For example, using the 'tree' command and then highlight all the files that have to be created / edited for this feature to work. It is just for better visualization of the modifications. I get something useful when calling git status.
Jan 27, 2021 I feel like I understand how to manage this quite well now The Python code and some of the xml seems to paste into the cli with loads of new tab characters, in vim I used ':set paste' to switch off auto indent. Doesn't happen with the yml though
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Jul 2, 2021 Clear explanation of the subject object_store_config_file: "{{ galaxy_config_dir }}/object_store_conf.xml.j2" should be object_store_config_file: "{{ galaxy_config_dir }}/object_store_conf.xml"
Jan 28, 2021 Easy to add local storage, the dropbox integration is good Warning: switching object store types will cause issues - suggest putting that at the top and emphasise that this is a tutorial that shouldn't be blindly followed on a proper install. The S3 section assumed quite a lot of knowledge - I didn't understand, but expect someone who manages data in an S3 bucket will!
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Mar 18, 2022 Is really cool to see lots of different admins pooling their knowledge and effort in this way From a voice control perspective, it would be useful if the hands-on gxadmin commands were in a copiable code block like they are in other tutorials – it really helps to be able to copy them with the single click. Also, the 'admin favourites' section could include the arguments for the functions listed, e.g. <job_id>, for a bit more clarity
Jul 1, 2021 Simple and clear The Hands-on: Adding a query did not work as the user ubuntu but had to be done as the user galaxy
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Jan 29, 2021 The whole concept of being able to separate training needs vs production needs is brilliant 3. We next need to configure this plugin in our job configuration (files/galaxy/config/job_conf.xml): Should be templates/galaxy/config/job_conf.xml.j2 to match rest of training?
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Jan 15, 2022 In-depth explanations and side bars of what the various commands are doing so you can easily troubleshoot and customize. There is an "error" in the example code for the Galaxy/FTP portion of galaxyservers.yml. if you intend to use separate upload directories (with email addresses as the folder name) for each user - as the tutorial indicates will happen - then the current code (below) will result in the uploads going into the parent directory "/uploads" instead of "uploads/user_email" . # FTP ftp_upload_dir: /data/uploads ftp_upload_site: "{{ inventory_hostname }}" Instead the code should be (add a "/"): # FTP ftp_upload_dir: /data/uploads/ ftp_upload_site: "{{ inventory_hostname }}" Took me a while to work out why it was going into the wrong directory. Also - it should be stated that there may be a newer version of the playbook that could solve errors/conflicts with newer operating system versions than those used in the tutorial. Also suggest highlighting parts in the code examples which should be customized to your server environment if you are using this as a guide to setup your own installation (primarily directories where stuff is located).
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Jun 8, 2022 The interactive tools perspective The requirement for wildcard SSL certificate and the poor support for fulfilling this requirement. This is a major issue for the deployment of Galaxy servers. From a historical perspective, before 2019, there were IEs. Not super easy to deploy, but doable with motivation and investment in Docker knowledge. After launching the new ITs, IEs became progressively useless and ITs stay either nice demos or running on very few big public servers. Even the latter is not so clear: for instance, usegalaxy.org.au is not really providing ITs, usegalaxy.org (!) seems providing it at first glance, but the Rstudio interface - for instance - remains full blank forever. Only usegalaxy.eu to my knowledge provides effectively running and usable generalist ITs (Rstudio, Jupyter,). Thus, on that matter, where is the initial slogan "data intensive analysis for everyone" ? Of course, I am not blaming the trainers and contributors to this tutorial in any way ! But I really think that the technical strategy relying on wildcard SSL certificate to get the ITs running should be discussed with the community as a serious limitation to their use and thereby their active development. As it stands since 3 years now, ITs are out of the possibilities of a majority of Galaxy server instances because too complicated to install.

Genome Annotation

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Nov 24, 2022 Short and precise, not more or less than what the title promises One setting in the JBrowse step isn't congruent with the most recent Prokka version anymore: can't configure "Produce Standalone Instance”: "Yes" maybe you can update this :)
Oct 10, 2021 quick and simple none
Apr 3, 2021 It seemed clear - just didn't work. I read the tutorial as I tried to duplicate it in Galaxy with a phage genome sequence. The tutorial did not correspond with what was in Galaxy. JBrowse did not work - no indication why.
Mar 10, 2021 It doesn't show you where to begin. It gives you steps but doesn't show you how to get to each step. Very frustrating
Feb 18, 2021 Simple and easy to demonstrate gene annotation using contigs
Jan 29, 2021 Concise and clear. Thank you!
Jan 8, 2021 The explaination about how to use Prokka JBrowse doesn't work with this parameters, you should update this tutorial
Sep 21, 2018 I am doing this tutorial 09/2018 -> the step using the JBrowse tool works only (at least in my hands) with this version: (Galaxy Version 1.12.5+galaxy0) i had troubles finding it (maybe the search does not work properly?)
Sep 21, 2018 I am doing this tutorial 09/2018 -> the step using the JBrowse tool works only (at least in my hands) with this version: (Galaxy Version 1.12.5+galaxy0) i had troubles finding it (maybe the search does not work properly?)
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Jan 26, 2022 nothing nothing
Oct 20, 2021 This tutorial is very helpful After the functional annotation how to recognise genes related
Nov 13, 2019 nothing everything no vid
May 12, 2019 Analysis for tutorial should be done on large datasets like genome from population rather than on individual genome.
Feb 27, 2019 The first steps of the tutorial are great, described in a simple and objective way. I was unable to continue from the "Hands-on: Run I look for the genome" stage. I looked for the BUSCO tool on the Galaxy platform but nothing was found. For this reason I could not complete the tutorial. It would be good to evaluate the availability of this tool or change this step of the tutorial so that we can finish successfully, thank you!
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Aug 5, 2022 List elements identified during the process of genome annotation.
May 23, 2022 proper description and arrangement. Results
Feb 17, 2022 The clear steps and explanation attached Some tools have not been found in Galaxy such as antiSMASH.
Apr 8, 2019 good description of what annotation is did not tell me how to do annotation using tools present here, would like a step by step instruction on how to do an annotation if I have a genome sequence
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Aug 23, 2022 everything.. thanks for this i cant find bowtie tools.. only bowtie 2, but the parameters described here are for bowtie.
Aug 4, 2021 very clear r code
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Mar 31, 2022 the sharing link is not working, so i couldnt share and create the group
Mar 15, 2022 super interesting ! especially the sharing part !
Jul 2, 2021 nice talk and gives a rly good overview of apollo/galaxy interface. thank you! explain what are all the data you add as input inthefirst step, do u rly need that much? in the tutorial we only use some of them
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Jul 11, 2021 Thanks for the detail explanation.
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Oct 11, 2022 What I liked most about this tutorial was the existence of explanations that helped in the interpretation of the various outputs produced by the software. The tutorial could be updated because I found that there are discrepancies between the tutorial and the Galaxy platform. Namely, the name of some of the tools and their location on the website differ between the tutorial and the current platform.
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Apr 3, 2022 A demo with a cripsr pool set who works (so many online pool screen CRIPSR tools do not work). so many command based installation do not work. Simply starting with MAGECK installation on python is just a nightmare, it does not install smoothly, and it seems thatthe original authors move on and do not care at deploying this smoothly to the community(only expert can use these code lines). I really appreciate the work here. It seems more applicable from any machine without all the dependancies, environments, expertise in coding and languages bug...... Should make mageck available in global galaxy and not just australia one. Could provide other datasets such as cripsrI or cripsA pool set to extend the range of trial for users to get accustomed with the pipeline.
Mar 25, 2022 everything because all was new for me Add more information in the lecture (describe more meticulously the CRISPR analysis)
Mar 15, 2022 It was super clear, and combine nice tools For me was not "intuitive" to have a test with two p-values (for negative/positive selection). That I do not know if it is pretty common in transcriptomic (and I missed it) or if it is non so commonly used and it was speciffically developed on MAGeCK test. If it is not commonly use I think that can be nice to include a brief description of the statistical test in the tutorial of the course.
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Mar 16, 2022 good explanation why masking is done

Imaging

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Introduction to Galaxy Analyses

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May 18, 2022 Easy to follow. Helpful examples.
Apr 1, 2022 it's was more clear and more relating than others i think a pdf explaining some notes would be ok
Mar 21, 2022 easy to understand and the tips are really usefull no idea
Mar 18, 2022 I never have even coded before! so easy to use
Mar 8, 2022 Easy to follow, user friendly for someone without background
Feb 9, 2022 very clear tutorial!
Feb 7, 2022 I liked the step by step follow up of results while doing the analysis
Feb 7, 2022 the simple and easy demonstration
Feb 2, 2022 The educational aspect and questions asked The last question has no answer
Oct 14, 2021 I love that you have to pay close to every little details for now nothing
Oct 11, 2021 How it shows you that you to make adaptable workflows
Oct 11, 2021 I especially loved how simplified the tutorial was, even as a beginner I was able to run my analysis and publish it. Thank You! It is fine as it is...maybe extra datasets to practice with.
Sep 1, 2021 good explaination difficult to say
Aug 12, 2021 the easy step by step guide nothing
Aug 11, 2021 Systematic Excellent
Aug 11, 2021 Automating workflows Add more analysis
Aug 10, 2021 Easy to follow. To the point!
Aug 10, 2021 training format
Aug 10, 2021 great organizing and illustrations more practice
Aug 10, 2021 clarity, information packed
Aug 10, 2021 It was very clear It is perfect!
Aug 9, 2021 The hands-on manual is very interactive More pictures on how to carry out the steps
Aug 9, 2021 It was very clearly explained. So even someone without experience, as myself, could go through this very easily. No suggestions
Jun 29, 2021 Completness
Jun 25, 2021 All Nothing
Jun 17, 2021 The explanation to implement each step nothing
May 23, 2021 clear and to the point
Mar 22, 2021 Easy to follow steps Where to go next button to jump into another training session
Jan 6, 2021 In a previous version of this tutorial a join was performed to add exon info to the number of snps. This step was removed in a later version of the tutorial.
Sep 11, 2020 I like the Galaxy tools and how well the tutorial explained what the purpose of the tools were in terms of the science itself. The tutorital should be upgraded and edited to ensure its correct. For example, telling reading to type "Column: 4" caused errors; should have only typed in "4" for it to work. This was addressed, but WELL after that part of the tutorial.
Jul 23, 2020 Everything :) this is incredibly illustrative and I feel so much more confident to use Galaxy now
Jun 29, 2020 Easy to follow. The comments were very helpfull
Apr 15, 2020 very easy to follow
Mar 30, 2020 failed at step of either join or count. column drop down was not available in count, so entered manually. when count applied, error on column sepecification
Mar 12, 2020 Explanation how to use UCSC browser to see user track
Feb 14, 2020 I appreciated that this tutorial used a smaller data set, so that the analysis went much faster. I also appreciated comments on what to look for if the analysis didn't work. I am a genetics instructor at a PUI, so this tutorial was at a good level for me to think about what I want to teach my students. At the section on "recovering exon info" it would be nice to prompt the audience to consider which data sets they should compare, and which columns should be used (maybe as a side activity). When viewing results at UCSC main, ideally it would be nice to direct audience something in particular to look for. There is a lot of data, which will definitely overwhelm my students. This is a meta suggestion....I'm going through the introductory tutorials one by one and found this one to be more introductory than the "peaks to genes" tutorial. I wonder if considering reordering tutorials (make this one the second on the list?) or naming tutorials would help audience. Great tutorial - I definitely appreciate your work on this!
Jan 28, 2020 The fact that it had a task in mind A bit more clarity on how to correctly indicate the column names would have saved me a lot of time trying different variations when "Column: 4" was not recognized as an input
Jan 2, 2020 Repeatable workflow for fresh man to this server. Further clarification to the function input parameter maybe need.
Dec 5, 2019 In general, it is good. For first time user, some instruction should include more details. Some guides are not clear.
Nov 29, 2019 very clear instructions
Nov 21, 2019 Easy Maybe automattically update to gencode updates, there is no genecode v29 anymore
Oct 16, 2019 Informative and easy to follow
Oct 9, 2019 Useful and easy to follow
Oct 8, 2019 details other cases
Sep 6, 2019 Very easy to follow Ability to zoom on the graphics
Aug 28, 2019 Easy to follow and useful
Aug 28, 2019 it was sufficient
Aug 28, 2019 Screenshots and clear colour coding made it extremely easy to follow Nothing - I thought it was great! :)
Aug 2, 2019 I liked how easily it flows, some concepts of biology are briefly explained, it helps a lot! Maybe add more examples, more explanations on the datasets used.
Jun 11, 2019 Good introduction to Galaxy. I like the worklflow function the most. Couldn´t really see what the results in the genome browser would tell me and how I apply this for my work.
May 30, 2019 The instructions were very clear and easy to follow It would be nice if there is more explanations on the significance of each step and what exactly is being performed when selecting different tools.
May 16, 2019 Ease of understanding Adding more examples of its applications and how it is used in real time
May 1, 2019 Instructive I do not know - I know only Biopython
Apr 25, 2019 explanations were very clear ! this is a bit too long
Apr 18, 2019 Fatal error: Exit code 1 () Error running sorter.py Command '(grep '^#' /galaxy-repl/main/files/030/998/dataset_30998511.dat) >> /galaxy-repl/main/files/030/998/dataset_30998729.dat' returned non-zero exit status 1
Feb 25, 2019 Very simple to follow and learn on my own
Jan 31, 2019 Very good explanations, good demonstration of Galaxy potential for begginer
Jan 14, 2019 Galaxy at usegalaxy.org ends up showing "the white screen of death" extremely often (10s of times during following this tutorial).
Nov 28, 2018 Easy to follow, but the task is not trivial! update some of the options and screenshots to be consistent with the latest version of Galaxy
Nov 28, 2018 Easy to follow Including some assignment or home work
Nov 4, 2018 One could add a section describing the use of multiple datasets, tags, etc.
Sep 27, 2018 easy to follow
Sep 27, 2018 I found it interesting and user friendly nothing for now
Sep 26, 2018 The presentation of the tutorial and the practicality of it The rate of update of the tutorial
Sep 14, 2018 very detailed and easy to follow, even for a complete beginner - great!
67 responses
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Detailed feedback
Date What did you like? What could be improved?
Aug 30, 2022 Biological explanations after a command. I think its great, but one improviment is add more image from Galaxy.
Aug 25, 2022 Most of the explanations and step were explained well but many icons in Galaxy have changed . An update will be appreciated. If USC browser is the main source , please have a detailed tutorial what all that stuff means . Thanks
May 25, 2022 It explained everything in simple language!!
Apr 29, 2022 interactive
Apr 7, 2022 It's easy, indexing and saving history is great tool Maybe, in this tutorial, using colors for different strand genes would be more easy to see in genome browser later
Apr 6, 2022 the fact that it gave definitions for things that could be unknown not really much. maybe make similar tutorials but for larger jobs
Mar 26, 2022 It was written clearly One place I think it could be improved would be on Create a reusable workflow from a history, under the Test Workflow part 2 (Examine the workflow run form) wasn't clear as the others and found it to be confusing.
Mar 22, 2022 Detailed description All are ecxellent
Mar 19, 2022 The detailed description I think that all are perfect
Mar 19, 2022 very simple and basics mode of explanation
Mar 19, 2022 User friendly and really hepful for novices like me
Mar 17, 2022 Explanations
Mar 16, 2022 The final percentage overlap could be provided so students can compare to make sure the results are the same
Mar 16, 2022 The practical easy-to-use guide
Mar 16, 2022 everything was so interesting, but workflow part is more fascinating. I think there is no need of the improvement every thing is so perfectly fine and easily understandable.
Mar 15, 2022 Ease of understanding and depth of explanation The videos are old and out of sync of the tutorial material in some cases. There is need for new videos to be developed
Mar 14, 2022 saving and re using the workflow more hand on activities
Mar 14, 2022 intuitive nothing
Mar 14, 2022 A single tutorial teaches to get information from UCSC, analyze them, view it in genome browser and asks us to use the pipeline to work on similar biological problems.
Feb 24, 2022 Nice Step by Step Tutorial Finding the tools was a bit difficult with the search bar. Somethings are a bit outdated.
Feb 22, 2022 Very detailed explained steps, which made the analysis very easy
Jan 27, 2022 An example full of information no
Nov 15, 2021 Detailed Explanation
Oct 15, 2021 Basically the fact that you can always get your way around None for now
Aug 3, 2021 Tools Detailed Explanation: how to use and details about the tool. Nill
Jul 15, 2021 Update to the newer version of Galaxy (new style)
Jul 1, 2021 Expaination from Dave was Fantastic, and I was able to have the Hands-on without any problem :D Nothing in my oppinion.
Jul 1, 2021 explanations which were easy to understand, explaining concepts well without going into overwhelming amounts of detail; defined any foreign terms clearly
Mar 11, 2021 It was clear and well structured. Nothing! Galaxy is awesome
Feb 26, 2021 The tutorial is hands-on, straight forward and easy to follow
Feb 26, 2021 The hands-on tutorial which is straight forward and easy to follow
Feb 16, 2021 Practical Error of concept of nucleotides vrs amino acids
Feb 16, 2021 The tutorial and the goals were clear
Feb 15, 2021 Overall good structure It is rather specific, a short introduction ahead on the tools and ideas might be helpful
Feb 15, 2021 Very clear presentation, the results are clearly explained helping bioinformatician/biologist to understand the output Some tools were not in the right column, maybe use 'search tools' instead of looking for tools in a specific section (when the tool is actually in another section). Especially for Galaxy beginners
Feb 15, 2021 Very informative.
Aug 3, 2020 Simple introductions to bioinformatics with easy to understand (for a non-biologist) explanation of gene/chromosome and other concepts. Nothing. This was great!
Jun 30, 2020 Easy to follow Nowadays the tool Intersect, it's no longer in the Operate on Genomic Intervals toolbox.
Jun 12, 2020 Very clear Slightly outdated, some tool locations seem to have changed
Jun 11, 2020 I like the brief but detailed and easy to understand instructions with explanations the section on Visualize the overlapping genes could do with some improvement. I struggled to understand what scale track was and how to click it at the begining but eventually got around it. Maybe other users found it easy but that was my challenge.
Mar 17, 2020 Steps are clearly explained
Feb 20, 2020 I really liked how this tutorial encourages its audience to try to figure out which tools to use and how to use them to address the question. Just before the section on "Examine the data" there is a [TODO] line that has been left in. Oops!
Feb 15, 2020 this .bed file contain more row than number of genes on chr22 ?!
Aug 23, 2019 Update the intersect phase since that tool is no more available
Feb 28, 2019 Broke down the concepts well. Introduced ideas one step at a time with good explanations that minimized jargon. And worked to make concepts tangible with hands on use of Galaxy.
Jan 16, 2019 Galaxy says it has ran the workflow, but nothing happens.
Sep 15, 2018 very detailed and easy to follow, thank you
72 responses
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Detailed feedback
Date What did you like? What could be improved?
May 7, 2022 topic is very important some steps are not cleared explained, workflow for this specific task and visualization tool is not working showing loading error
Apr 1, 2022 detailing make an upgrage to server and do a video if possible
Mar 30, 2022 it was engaging to use of terms and examples so a first time contributor could follow along
Mar 15, 2022 The hands-on material is really well thought and it really gives us confidence in doing this type of analysis. It is very easy to follow through. There were two steps where I fumbled, one was when I tried importing the genes from UCSC browser it opened in the new history, I feel one link to paste that to current history tab would be beneficial, secondly, I was literally searching for Group tool under the workflow, then when I expanded the list then I could find it.
Mar 10, 2022 easy to understand with easy steps
Jan 20, 2022 How the each and every step is shwon with the screenshots. Just what an beginner needs. :)
Jan 5, 2022 guidelines are clear / no questions are left unanswered
Jan 3, 2022 Not yet completed This is how the output of get flanks are stated in the tutorial: For regions on the negative strand e.g. chr1 8349819 9289958 this gives chr1 9279958 9291958. However what I am getting is similar to the results of the + strand; the promoter regions lies between 8347819 and 8359819; it seems to me that get flanks did not recognize between the + and - strands
Nov 24, 2021 the concept. multiple issues with platform - loosing (they are not on the screen) history buttons, tag buttons, Once I brought the UCSC file in, I no longer can find the gz file - maybe it is supposed to be merged, but that is not what the tutorial showed. There was a disclaimer that said 'results might be different' but there were no Chr 21 to rename on the file. A little video showing what to expect might be more helpful than the icons in the description. I see it was updated in early November, but as a real beginner, this isn't any fun at all and very frustrating.
Oct 18, 2021 learning of workflows
Oct 13, 2021 It was well detailed only a few to crack about. some illustration needs to be more detailed
Sep 7, 2021 Great introduction to Galaxy, simple, easy to follow Clearer explanation of why something is done. Perhaps similar to the 'tips', added detail for those that want to delve deeper. Also more up-to-date visuals of the steps involved The final output is a little lack-lustre. maybe a nicer visualisation option to cap off the tutorial (kind of like a nice 'reward' for effort)
May 11, 2021 It is a very clear step by step, well defined tutorial. The difference between method 1 and 2. The peak summit concept may need more explanation.
Mar 12, 2021 Part1, the Repeat workflow is not working. The manual is different from for actual workflow in galaxy.
Jan 22, 2021 I think it's supposed to be an introductory course, but it got too complicated and theoretical. I am familiar with sequencing terminologies but I didn't understand what do you mean bye peak and broadness of the peaks!! Thanks BTW I think the theoretical part of this tutorial should be explained in details
Jan 1, 2021 everything excellent as is
Dec 1, 2020 the easyness and biological meaning of the data some data import, from UCSC for example, some times fail and ends up in a different history and logges me out
Nov 27, 2020 The tutorial should probably be updated to use the latest versions of tools
Nov 18, 2020 This was confusingly written. It's use of jargon and short cuts limits its access to those not trained in bioinformatics and coding. The presence of multiple authors on this piece may have led to this confusion, as the person that wrote the first two was very clear.
Sep 28, 2020 everything hardly
Jun 29, 2020 very easy to follow
Jun 24, 2020 everything
Jun 11, 2020 Very little Incredibly hard to follow
Apr 7, 2020 Building more complex workflow from small steps. Hands-on: Count genes on different chromosomes - needs to be updated, instead of Column 1 only 1 should be used. Otherwise the analysis fails.
Feb 25, 2020 it was easy to understand how to do it why do i do it?
Feb 25, 2020 detailed explanations; step for step -
Feb 14, 2020 The format of the tutorial is easy to follow and the instructions are clear. The organization is such that it was easy to find where I had left off from the day before. I ran into technical difficulties that I cannot resolve; it's hard to say whether this is due to the tutorial itself (visualizations hasn't worked yet; the first analysis went fine, but the second yielded an empty data set). Also, it took FAR longer than 3 hours; I do wonder if having a smaller mock data set would have helped this problem. I'm trying to learn galaxy in order to incorporate an activity into my undergraduate course. This tutorial seemed more relevant for training people who will use galaxy for their research. A toned-down version with a smaller data set, perhaps without so many necessary file preparation steps would have been appreciated for my particular goals. Having said that, I am guessing I am not the target audience, so I can see how this tutorial would be very useful for another audience.
Feb 12, 2020 in Hands-on: Adjust chromosome names incolumn must be just number not Column:1 first part could explain more about chip seq and input data
Sep 29, 2019 Clear and easy to follow More results illustrations
Sep 28, 2019 The easy to follow structure of the guide plus the additional links provided in the Tips sections. I recommend adding more images of the data being analysed for part 2 section Repeat workflow, 'Run a workflow with changed settings'. This would have been helpful to be able to compare my results with the guides.
Aug 21, 2019 not working with the bedtools intersect intervals (the other tool is currently not working) Update
Aug 15, 2019 I didn't have the time to like it since the intersect command is not working :( I would love it to work, the tools changed in the meanwhile and it need to be updated cause it is not working anymore for some not clear reason . Most probably there is a problem with the UCSC file (I changed any kind of parameter on the interval file and i get always the same error).
Mar 5, 2019 most but if the files that need to be downloaded do not exist at UCSC, this tutorial is useless go through the process and correct
Feb 25, 2019 Very clear instruction and step-by-step explanation some small exercises or quizes
Jan 8, 2019 Step by step introduction and repetition of features
Nov 22, 2018 Easy to follow tutorial We did not realize the 00000000rik names were also gene names, so we spent some time thinking we did something wrong...
Nov 22, 2018 easy to follow individual steps Chipseq data seems a little more complex than more 1-dimensional seq reads (DNA/RNAseq), so would seem to me that starting with e.g. RNAseq analysis could be more logical
Oct 17, 2018 Nice clear , very informative airconditioning less cold
Oct 17, 2018 it is clear would like to have example outputs for important steps, so if i made a mistake in step 7 i don't have to find out in step 19 and go back to revise everything. I can just use the dummy dataset for step 19 to continue and finish the practice
Oct 17, 2018 scope, topic and clarity of tutorial
Oct 8, 2018 More visual examples
Oct 2, 2018 simplicity pick a relevant induction based on your needs
Sep 17, 2018 Well-structured and helpful More information on the flanking region tool (how it works)
Sep 17, 2018 well explained maybe by adding more pictures next to the explanations?
Sep 17, 2018 Well structured, easy to understand.
42 responses
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Detailed feedback
Date What did you like? What could be improved?
Jun 18, 2022 it can be more better how do you get the end result was not clearly explained
Mar 28, 2022 The tutorial was instructive and easy to follow. I loved the variant calling and annotation.
Jan 6, 2022 I am getting an error : Warning unsupported media type (415) while trying to upload the reference genome using the link "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/858/895/GCF_009858895.2_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna.gz". And I am not sure which file type to pick when trying to download from NCBI using the accession number "NC_045512.2" provided.
Dec 23, 2021 Step by step nature More explanation of what i am actually doing at each step
Aug 21, 2021 Good for beginners More explanation and examples
Aug 17, 2021 The simplicity of the step by step guide If the tool needed for each step is clearly listed
Aug 12, 2021 The step-by-step analysis Clear sound/tone of presenter
Aug 12, 2021 Clear and systematic Instructions can be more specific (e.g. names of tools)
Aug 11, 2021 The way Galaxy is able to bring all these bioinformatics data possible to the public.
Aug 9, 2021 There was so much info about FLAG and CIGAR which was not relevant for the exercise. I would have rather learn more about VCF which was important as well as all the meanings behind the headers of the final dataset like DP, AF, SB, DP4, EFF.IMPACT etc. How was read group information relevant for this exercise? I did not understand this. Please state it more clearly in the process if it is relevant. The search did not often find the specific tools but gave 100 options if the name was not specific. Sometimes the full description of the tool was added at the end of instruction but in some cases it was absent which made it more difficult to find the correct tool. The info about duplicates is messy and confusing. Either leave it our or explain/link the info about duplicates more clearly and more in relevance to the excercise. State the point of the final outputs. What can we do with this data, how can this information be used in relation to the covid pandemic? What are the downstream analysis options after this etc.
Aug 3, 2021 detailed explanation of the steps for analysis Also provide information of other tools for the same type of analysis
Jul 8, 2021 good and clear explanation of formats and data -
Jul 8, 2021 protocol Analysis part can be explained a bit detailed
Feb 22, 2021 Very good material
Feb 15, 2021 Complex but very interesting!! All steps are clearly explained. As i said, the data analysis was complex. So detailing the results would have helped to better understand.
Feb 3, 2021 Background information about NGS data progressing and file types Perhaps could includes some information about how to view or check the SAM/BAM file.
Oct 19, 2020 clarity
Mar 24, 2020 Video are difficult to follow
Aug 27, 2019 Please date this content. Is it out of date? It does not mention kallisto, sleuth or salmon. Are these available in a cloud somewhere? Are they better?
May 24, 2019 all of it add example with bowtie2
Apr 30, 2019 I liked the videos. I would suggest to make the videos longer and theory shorter.
Jan 22, 2019 awesome and answered many of the questions in my head nothing I can think of
Jan 17, 2019 Explanation of theoretical basics. Links to additional resources. Mark Duplicates step fails: Fatal error: Exit code 1 () Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/022/055/22055178/_job_tmp -Xmx7g -Xms256m 11:37:37.876 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/cvmfs/main.galaxyproject.org/deps/_conda/pkgs/picard-2.18.2-py36_0/share/picard-2.18.2-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Thu Jan 17 11:37:37 CST 2019] MarkDuplicates INPUT=[Filter_on_data_7__Filtered_BAM] OUTPUT=/galaxy-repl/main/files/029/341/dataset_29341054.dat METRICS_FILE=/galaxy-repl/main/files/029/341/dataset_29341053.dat REMOVE_DUPLICATES=true ASSUME_SORTED=true DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true ADD_PG_TAG_TO_READS=true PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Thu Jan 17 11:37:37 CST 2019] Executing as g2main@roundup55.tacc.utexas.edu on Linux 3.10.0-693.21.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_152-release-1056-b12; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.2-SNAPSHOT INFO 2019-01-17 11:37:38 MarkDuplicates Start of doWork freeMemory: 248936480; totalMemory: 259588096; maxMemory: 7265714176 INFO 2019-01-17 11:37:38 MarkDuplicates Reading input file and constructing read end information. INFO 2019-01-17 11:37:38 MarkDuplicates Will retain up to 26325051 data points before spilling to disk. [Thu Jan 17 11:37:38 CST 2019] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=382373888 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record 262, Read name M01368:16:000000000-A3M99:1:2114:3862:13382, bin field of BAM record does not equal value computed based on alignment start and end, and length of sequence to which read is aligned at htsjdk.samtools.SAMUtils.processValidationErrors(SAMUtils.java:454) at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:812) at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:797) at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:765) at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:576) at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:548) at picard.sam.markduplicates.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:495) at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:232) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:282) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:98) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:108)
Nov 27, 2018 The explanation is very clear and concise, thanks!
Nov 17, 2018 Clear and consise
Sep 27, 2018 makes life easy very good
348 responses
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Detailed feedback
Date What did you like? What could be improved?
Nov 17, 2022 Easy to follow for the most part. Needs to be updated to the current galaxy settings.
Oct 25, 2022 everything nothing
Oct 25, 2022 La manera que explica Me parece que estuvo bien
Oct 25, 2022 The complete explanation
Oct 25, 2022 images make it easy to undestand maybe you could add videos to help undestand the steps
Oct 24, 2022 The tutorial is simple and easy to understand. The instructions are clear and the images help the student to know what to do. One thing that could be improved is the location of some filters due to is a little bit confusing.
Oct 14, 2022 que explicara mas a fondo el uso de las demas herramientas con ejercicios
Oct 12, 2022 simple and easy to follow, although some of the icons have changed in the updated version Just updated screen shots
Oct 11, 2022 The wheel symbol in the history menu has changed to an arrow down. Also, the way to see the histories side by side has changed.
Sep 28, 2022 I really liked, that I could actually try it out.
Sep 25, 2022 I appreciated the descriptions and the format of it, like bullet points, etc. I think more pictures would be valueable since it is a bit hard to navigate at first, especially during the 'workflow' i got a bit confused
Sep 15, 2022 Easy to follow, encouraging to continue exploring First time I run the QC analysis it took more than 1 hour, it would be great to have a time tracker so we can estimate the duration of each analysis (Second time I did the analysis it run in about 2 min)
Sep 12, 2022 Easy to follow Couple of things out of date: view all histories is now in the menu and "Click on galaxy-gear (History options) at the top of your history panel and select Extract workflow." no longer a galaxy-gear icon but a drop down?
Sep 12, 2022 It was doable by a wet lab scientist without prior experience in analysis!
Sep 12, 2022 Simple, clear
Aug 4, 2022 Everything Not much at all
Aug 4, 2022 I loved the fact that although this is not in-person, it was more interactive and practical.
Jul 20, 2022 clarity of each step a short video can easy to complete this workflow and help peopless to learn it in much less time
Jul 14, 2022 Easy to follow steps
Jul 9, 2022 Thorough guide with plenty of time for users to try. To me it's simple enough to follow all the instructions, no improvement needed.
May 24, 2022 the details
May 21, 2022 Platform is simple enough to follow and the steps are well-explained. When I run the tutorial with Windows as an OS everything ran smoothly, but when I was on Ubuntu linux I had issues with the window that I had to load the dataset. The options for pasting the data, etc. were not visible at all and I could not do anything for it.
May 16, 2022 I like the clarity of the pictures used in describing the different steps There is nothing needed to be improved. The tutorial is excellent
Apr 30, 2022 easy explanations
Apr 27, 2022 It was simple (great for the first aproach), really clear and usefull
Apr 25, 2022 The tutorial is Practical and easy to understand I think in will be usefull to include another ways to upload files
Apr 8, 2022 Detailed and accurate. I have no suggestions
Apr 7, 2022 clear directions. screen shots help
Apr 4, 2022 It was straigthforward and had animations to guide you. I think it's missing some basics of Galaxy.
Mar 31, 2022 Maybe if you in "Convert your analysis history into a workflow" change the photo for how it should looks - where you write what, I was bit confused. This could be better for me.
Mar 30, 2022 Simple explanation with helpful images to provide guidance
Mar 29, 2022 It was simple and easy to follow It would be great to have some real examples of how this can be applied to your data
Mar 28, 2022 i like the fact that it took me from a newbie to having some level of knowledge on how the galaxy interface works. As much as i really enjoyed this article, i actually struggled with understanding the "Convert your analysis history into a workflow" part, as it needed more pictures or more specific descriptions at number 4 and 5 guide steps. i had to read it over and over, and do some brain work to figure out what the author meant. if this could be improved for upcoming readers like me, it would be much appreciated and will lead to more productivity on our end.
Mar 28, 2022 I loved the workflow aspect of the platform.
Mar 27, 2022 All the steps were clear and precise. Somewhere I found video demonstrations too, which was unexpected. The concept of collapse and expand features were eyecatching. Yes, at the end if we have a video covering the entire steps, it could be used as a quick revision of the steps we did above.
Mar 24, 2022 hands on run everything is perfect
Mar 23, 2022 Easy to follow and grasp concept Not sure
Mar 20, 2022 it was understandable
Mar 17, 2022 Step by Step learning
Mar 16, 2022 The hand one are very easy and clear. Allow students to answer the questions whithin the hand on then they can compare with the available answers
Mar 7, 2022 It is really hands on
Mar 7, 2022 It is very detailed tutorial and easy to follow also for beginners like me
Mar 7, 2022 Step wise instruction It was perfect for me.
Mar 7, 2022 Easy to follow and focused on the basics
Feb 21, 2022 every step was clear to follow follow-up video for people who have network issues so that they can watch and catch-up fast
Feb 18, 2022 It was very precise and easy to follow. I think it's excellent as it is.
Jan 14, 2022 The way they teached us. Very Short tutorial, needs to add some other tools alo.
Dec 20, 2021 Muy claras las explicaciones Todo está bien en este tutorial
Nov 30, 2021 How easy is to follow the instructions Probably adding more languages, but the english it's totally understandable
Nov 29, 2021 Very well explained, very visual Maybe add some more information about the type of analysis we're running
Nov 28, 2021 It is very clear and easy to follow anything, it is what it states: a short introduction :)
Nov 6, 2021 Ease of explanation Nothing I think
Nov 2, 2021 Everything More Videos
Nov 1, 2021 La facilidad de interfaz que tiene la pagina, se entiende muy rápido y claramente los pasos que se deben realizar para cargar un documento, y el como se visualizan, analizan e interpretación de los diferentes datos. Aun me toca explorar la pagina por el momento este tutorial introductorio es bastante útil y fácil para quien apenas esta escudriñando con el programa.
Oct 31, 2021 Simple, makes the user understand how to use Galaxy More user friendly data examples for any kind of student who is not from biology background to experiment with and analyze
Oct 13, 2021 I liked that the tutorial was very informative, I learnt a lot of new and exciting things. It was short but had a lot of examples packed in it. I also enjoyed trying trying different analysis on the platform. 1. In the "Upload a file" section. I suggest that the disclaimer should be added so a user knows that they would not be able to upload a file if their email is not verified. 2. I appreciate that a lot of information was included in this tutorial, however I believe that the page could be improved to engage a reader more. The spacing between the sections and the fonts and colours are quite confusing. 3. The "Use a tool" could be more descriptive. No 3 : No change in the other parameters could be changed to " No changes should be made on the other parameters" . I believe thie would be easier for a user to understand. 4. I am also not sure why we have a "Questions" section. It deviates from teaching a user how to navigate the platform to explaining the analysis of the result. I suggest this is moved to a follow up section. 5. The icons in "Hands-on: Re-run the tool" section should be updated to tally with what is currently in use. 6. I believe the tutorial should be more descriptive. More pictures should be used as seen in "Look at all your histories" section. Thank you.
Oct 13, 2021 I love that h training material was straight forward and essay to understand and comprehend I had a major challenge, as while using the platform to learn step by step, on the material provided, I created a Galaxy account, I got handily with the platform , it was said after uploading a file, go to tools to search for FastQC and execute, but it was not bringing out parameters as seen on the project training material, likewise Filter by quality. There by preventing me from going further with the short introduction to Galaxy. In a Nutshell what was listed in the training material is not popping up when I search for this tools. I do not know what I may be doing wrong
Oct 12, 2021 It like the different tools and the much they can do. it makes analysis easy If the "Tools" on click or hover and give a little info on what the tool does, it would be nice.
Sep 1, 2021 Steps were clear and friendly
Aug 27, 2021 the instructions were detailed and precise i think it was fine
Aug 17, 2021 It is reproducable
Aug 5, 2021 The explanation was clear The example file does not work
Jul 30, 2021 Really easy to follow and understand what I was doing. Very up to date also. Better than many online tutorials that I have done. More explanation of what the outputs mean.
Jul 11, 2021 clarity and simple
Jul 8, 2021 step by step explanation for each task
Jul 6, 2021 All the instruction provided were user friendly, even students without the knowledge of computer can easily learn the tool just by follwing instructions
Jun 26, 2021 Simple and Elegant
Jun 25, 2021 Clear and concise; had images to show where things are; I got a little confused at the end where it said to click on Analyze Data in the top panel (step 3 in the "Look at all your histories") and could not find a way back without clicking the home button again.
Jun 19, 2021 It helps me to understand about the basic of data type -
Jun 2, 2021 very clear and complete
May 22, 2021 well explained!
May 21, 2021 It was clear and easy to follow
May 12, 2021 The trimming and filtering part is the most important stage of RNA-seq data analysis. Generally, adapter sequences are not given with SRA data in NCBI . Therefore, I was shot in the dark while using the trimmomatic, cuadapt and other tools whose results are not that much satisfactory. The information given in the tutorial seems to work for one of the messiest data. I think it would be great to see usage of filtering and trimming tools on one or two messy data. It will give us insights about how to deal with such data
Apr 20, 2021 Good for a beginner
Apr 14, 2021 It was easy and great with visuals as well
Apr 9, 2021 All aspects: clear, step by step illustration.
Mar 22, 2021 easy to follow
Mar 11, 2021 It's very precise and explain the most important characteristics of how to use the platform
Feb 23, 2021 Easy to follow and clear
Feb 18, 2021 How easy and friendly is the tutorial Nothing
Feb 17, 2021 Easy to follow We use FastQC. it would be nice to have some information about "Contaminant list ", "Adapter list", "Submodule and Limit specifing file" etc
Jan 29, 2021 Each part was beside its example. Add more images to each part and more questions to assure learning.
Jan 19, 2021 it's cleanness and clarity and simplicity. it is ideal for start
Dec 28, 2020 Excellent step by step instructions
Dec 27, 2020 Yes, but I needed more of NGS data analysis and interpretation Include thoughrough analysis of sequencing data eg finding a gene of interest, SNP, QTLs, marker trait associations etc
Dec 21, 2020 Everything was perfect! Nothing specific.
Dec 2, 2020 It was very visual and easy to follow
Nov 29, 2020 Hands on training Hands on training
Nov 29, 2020 Very clear step by step instructions with good visual cues and tests along the way to verify I'm doing everything correctly. I can tell this is going to reinforce good habits and logical thinking later on in your students. Really nice job.
Nov 28, 2020 Everything was clearly mentioned, making it very easy for beginners
Nov 25, 2020 very simple Thank you
Nov 18, 2020 Clarity of screen shots, simplicity of instructions, very little jargon Define what the quality of the reads means and why it's important
Oct 30, 2020 simple and clear no more
Oct 24, 2020 easy to follow more info on how to search for tools among the thousands of results
Oct 9, 2020 clear step-by-step the filter by quality tool does not appear in galaxy, unless I run it from the workflow associated to this training
Oct 2, 2020 Easy to follow
Sep 29, 2020 Very easy to follow Nothing
Sep 29, 2020 Simple to follow The link to the data is not owrking
Sep 11, 2020 Its comprehensive
Aug 20, 2020 The detailed step-by-step commands
Aug 10, 2020 Easy to follow
Jul 28, 2020 So clear
Jul 28, 2020 So clear
Jul 20, 2020 Easy to follow. Good use of pictures as a guide. Maybe include a video at the end doing all this.
Jul 11, 2020 Simple to follow I used the docker image and forgot to login, so I couldn't find the history rename / add new history options
Jul 8, 2020 Simple and clear!
Jul 6, 2020 I couldn't find "filter on quality" in the tools
Jul 3, 2020 Very easy to follow because of images with screen shots
Jun 29, 2020 easy to follow
Jun 25, 2020 It was helpful to learn to upload data. The tools no longer are found, that could be improved/
Jun 25, 2020 very detailed
Jun 24, 2020 It's a very simple and objective tutorial Images (prints of screen) of the tool parameters configuration screen would be of great help. Only the name of parameters is placed that we must changed, but, I believe that the screen print with these parameter and de value whould much more interesting mainly for very novice users like me.
Jun 19, 2020 Being able to follow through. Some links with good explanations to what these new bioinformatic terms are for beginners . Overall, it was great, thank you!
Jun 9, 2020 It was a very good explanation!
Jun 7, 2020 it includes a lot of details it will be better to include more exercises
Jun 1, 2020 Hands-on
Jun 1, 2020 Well explained/detailed
Jun 1, 2020 everything works as expected
May 15, 2020 questions and answers not sure
May 15, 2020 It's easy to understand.
May 8, 2020 clarity of the text improving my knowledge about galaxy panel
May 5, 2020 Having comprehension questions after each part of the lessons
Apr 25, 2020 It is simple and easy to follow.
Apr 17, 2020 Very easy to follow and good reinforcement
Apr 17, 2020 Very easy to follow and good reinforcement
Apr 15, 2020 Great that a URL was provided in case of not having a dataset to analyse yet. That made it possible to get "hands on". But also nice visualizations with pictures and the video, and good examples of how to search for the tools, how the three windows are arranged and how to navigate between the different histories. On the top of my head, nothing.
Apr 9, 2020 step by step approach adding more pictorial description of for example the exact place of the tool in the tool search, it took me long to find the tool I needed, and they didn't have that monkey-wrench image next to them
Apr 5, 2020 Clear and easy explanation with exercise.
Apr 4, 2020 the detailed descreption using a power point or video to visualize the steps in galaxy
Mar 24, 2020 The picture examples were very helpful. Information could be described more thoroughly.
Mar 23, 2020 simple, informative, easy first step by step guide
Mar 23, 2020 easy to follow, great visual aids
Mar 18, 2020 very basic. I need that How do you get back to a single history showing and the other two panels
Mar 3, 2020 The clear and short convenient characteristics nothing
Feb 21, 2020 every bit of it it was cool, and the best I think
Feb 18, 2020 Very easy to follow the instructions
Feb 11, 2020 Very Informative. Looking forward to it. Even for beginner as i am, i can using a galaxy without any problem. Thank you guys :) More analysis. Like whenever we'are using a tools, and it has a data view in it in the middle viewing panel, like QC, what is the number mean by all the statistic coming. Youre the best!
Feb 10, 2020 I liked the well-labeled comments/questions/hands on sections. Great level for beginners. There were some very slight differences between my window and the windows shown here, but honestly, I think this problem is unavoidable, and also it is good practice for people to struggle a tiny bit to figure out exactly what to click on. So...no improvements!
Feb 8, 2020 clearness a brief intro to IPython
Feb 7, 2020 logical flow of info what types of data can be processed having what type extension?
Feb 3, 2020 It's simplicty, I will use the images for my presentation as it's much faster than the slideshow.
Jan 27, 2020 Easy to follow and helpful Maybe more tips about what's important in setting criteria to filter the data; reasons, general practices...etc.
Jan 15, 2020 Very clear
Jan 14, 2020 detailed explanations and easy to follow
Jan 13, 2020 The variety in options when it comes to software
Jan 8, 2020 It is easy to understand and I hope I can start this tool easily.
Jan 2, 2020 The questions, pictures, easy explanations, AMAZING!! Update for updated version of Galaxy?
Dec 31, 2019 simple, informative and straightforward
Dec 27, 2019 all of the web
Nov 28, 2019 Straightforward and easy to follow
Nov 28, 2019 very good step by step instructions explain what the each step is doing to my data in this particular example
Nov 28, 2019 Quick and easy to follow!
Nov 25, 2019 easy to follow some guidance on the graphs that are generated and what they mean
Nov 19, 2019 C'est très bien expliqué
Oct 17, 2019 very helpful visualizations for tools inputs and outputs Not that I know of
Oct 10, 2019 for some reason the filter by quality tool did not appear :( but the tutorial was fab!
Sep 19, 2019 The step by step
Sep 11, 2019 The step-by-step guidance with explanations.
Sep 11, 2019 The simplicity and practicality of the tutorial More exploration of the data analysis to aid those who are not familiar with biological data (e.g. brief explanation of FASTQ and how to interpret it)
Sep 1, 2019 The step by step teaching More publicity to make this fantastic site more popular to bioinformatic field
Aug 19, 2019 thorough
Aug 14, 2019 Simple and clear
Aug 14, 2019 User friendly multiple ways of importing data in the introduction
Aug 7, 2019 Super simple and interactive
Jul 28, 2019 a very clear and concise introduction. The history names in fig 1 could be showing as the next-analysis and my-analysis.
Jun 23, 2019 the layout was great will not know until I work on my own data
Jun 14, 2019 almost all of it worked like the tutorial, very helpful the Filter by quality function was not on the program
May 31, 2019 simple and easy to learn
Apr 27, 2019 It was easy to follow and very clear
Apr 22, 2019 Very straight forward and convenient to catch up! None
Apr 22, 2019 Very graphical and easy to follow If you make a question, include always the answer with an appropiate explanation to make everything clear. Why in the case you use the 36 filter there are so many reads discarded? Do not Forget most of people is the first time they work with this online tool.
Apr 21, 2019 The detailed explanation
Apr 16, 2019 Tutorials are up to the point as the interface is user friendly If the tutorials could be downloadable, it could be a great help
Apr 10, 2019 everything
Apr 6, 2019 It is simple, clear and has materials for training.
Mar 22, 2019 the way it presented
Feb 13, 2019 Simple and easy to follow
Feb 12, 2019 Clear and concise instructions Nothing really,
Jan 23, 2019 Images with arrows, and short answer questions (made sure I was on the right path). The icons in the text were also a nice touch. I found the boxes around each of the big steps a little distracting. They are not necessary for the transition between the steps. The large headings are enough.
Jan 16, 2019 Easy to follow and use
Jan 13, 2019 No ambiguity and it showed some basics. Liked the labelled images.
Nov 19, 2018 Simplicity Nothing
Nov 1, 2018 This made using Galaxy very simple. This should be the first tutorial that shows up, even before the longer version as now I would feel more comfortable doing the long one whereas that one was overwhelming at first.
Oct 29, 2018 Easiness, You could link to short description of what a fastq format is, etc... and warn that Filterbyquality sometimes is not present. I could not find it. I use FilterFASTQ instead
Oct 18, 2018 explorations, explanations
Oct 18, 2018 Intuitive and well executed. Images were useful in following the flow of the tutorial. There is no answer to the question under the section entitled 'Re-run that tool with changed settings'. A 'Done' button does not appear in the view history screen as well.
Oct 18, 2018 Detailed explanation with screenshots!
Oct 18, 2018 Easy to follow with great pictures and arrows and labels none
Oct 18, 2018 Easy to follow and understand
Oct 10, 2018 step by step introduction, everything is very clear and easy to find some buttons do not exist (anymore)? Like in "Look at all your histories" under 3. at the top line there is a "done" button - this was not displayed when I did it. That is not a tragedy but it can be confusing....
Oct 8, 2018 The good explanation and visual help
Oct 8, 2018 Very straight forward Nothing
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Jul 9, 2022 more detailed form example was not explained clearly
Jan 20, 2022 nothing Does not tell me how to get FreeBayes data from Galaxy into IGV. IGV states that it cannot recognize the file. I have used these programs before, but something is different now.
May 7, 2021 It is not clear which files to choose, because "C2C12" clearly isnt available.
Feb 12, 2020 It is easy to follow and summurazing many tools features as much as possible. A real-life and frequently performed case tutorial could be shown for demonstrating what could be done in IGV.
Aug 22, 2019 RNASeq of C2C12 not available
Feb 25, 2019 Cannot find C2C12 file
Jan 15, 2019 Actually show some use-cases (there is only one and i am unable to load ENCODE data)
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Nov 4, 2022 the flow of presentation
Jul 27, 2022 the interaction of images and descriptions more images of the interface step y step
Jun 30, 2022 learning how to use a workflow on a different dataset
Jun 17, 2022 Ease of use
Jun 15, 2022 Nice and understandable! I'm a software engineer tasked with setting up and administrating a Galaxy server, so I don't have a bioinformatics background. However, I was able to understand this tutorial and now know why Galaxy is such a powerful tool!
Apr 29, 2022 hands on
Apr 27, 2022 It was easy to follow but learn usefull things
Mar 30, 2022 the presentation was staight to point there is an important feature that differs in the tutorial, the analyze data button is no longer accessible after the doing a workflow editing
Mar 29, 2022 Steps were so systematic and to the point i think it needs so much clicks but the good point is that you dont need to right that much
Mar 29, 2022 The best thing about this tutorial is how clearly all the steps have been laid out. As a new user, it makes it very easy follow along and get familiar with this platform. I didn't face any issues following this tutorial. One can follow it verbatim.
Mar 26, 2022 It is very easy to follow Its great for a beginner and don't think there is anything to improve.
Mar 16, 2022 The graphical data presentation and workflow set up
Mar 15, 2022 really loved the simplicity of the processes
Mar 14, 2022 the pace
Mar 14, 2022 Very informative and in depth without being boring!
Feb 22, 2022 It's clear and that take us by the hand to learn how to use galaxy. maybe make a youtube video to show all this tutorial
Feb 13, 2022 step by step explanation IT would be very useful to indicate that a tools used in the exercise are not accessible from all galaxy sites.
Nov 17, 2021 super nothing
Nov 10, 2021 Easy to follow and provides good grounding in Galaxy use Could the tutorial please be updated to avoid a common "error". The tool Group isn't recognised on usegalaxy.* services in the Tool Search as the search ID is tagged as "grouping". This is a fix in Galaxy core code but maybe a short work-around is to make mention in this tutorial that this tool can be searched for by the term "grouping"
Oct 21, 2021 Re-usability, Usages and all are awesome Wokflow creating, checking , unchecking while editing are little bit confusing to me
Sep 9, 2021 Easy to follow step-by-step instructions
Sep 9, 2021 Hands on tutorial, that makes learning easier Can probably expand the training to involved more complicated thing. Maybe saperate training
Jul 1, 2021 Its a quite good tutorial nothing feld sofar
Mar 4, 2021 The instructions are very detailed and clearly presented. Some pictures in the tutorial are not up-to-date.
Mar 2, 2021 Very good guiding cant think of something..
Nov 19, 2020 Very clearly written and helpful. I didn't see the advanced options for graphing until i played with the versions.
Nov 12, 2020 Nice and quick introductory course to Galaxy. I also really liked the breakout room idea.
Oct 8, 2020 Easy to follow steps and control examples. Sometimes locating certain tools/features on the web interface was like looking for the needle in a hay stack - especially true for the "upload data" button.
Jul 29, 2020 Well written explanations, easy to follow, highlights value of the project well Sometimes different tool versions available with identical names but different input options, that was slightly confusing.
Jul 27, 2020 I had problems with rerunning the dataset (diamond). Please further specify the parameters that should be used (It was asking me to insert column parameters in the "unique" part of the last task)
Jun 30, 2020 Very easy to follow tutorial. With usefull tips
Jun 22, 2020 Clear directions for execution and correlation of results.
Mar 26, 2020 Error when I followed instructions When I set “Data point options”: User defined point options “relative size of points” to 2.0, I got an error "Error in alpha * 255 : non-numeric argument to binary operator Calls: ggsave ... validGP -> numnotnull -> alpha -> <Anonymous> -> encode_c"
Mar 26, 2020 Error when I followed instructions When I set “Data point options”: User defined point options “relative size of points” to 2.0, I got an error "Error in alpha * 255 : non-numeric argument to binary operator Calls: ggsave ... validGP -> numnotnull -> alpha -> <Anonymous> -> encode_c"
Mar 23, 2020 extensive, simple, step by step in section "Visualize Iris dataset with Scatterplot w ggplot2" using the Data point options as user defined point options (relative size of points”: 2.0") originates error. Leaving default parameters corrects error.
Mar 16, 2020 Learn how to run statistics
Feb 7, 2020 introduce the tutorial with a statement of what type of data is being processed. Only when I saw a picture did I realize that your processing a flower called iris.
Feb 7, 2020 It was more advanced than the other introductory tutorial I had read.
Nov 11, 2019 The hands on exercises The images about the diamonds are not very legible
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Nov 12, 2022 Detailed explanations/tips/examples.
Oct 23, 2022 The simplicity and the start level, you can start in a very basic level. There is sth you have toke take in mind, when you copy the dataset a space is coppied at the beggining of the link. With this space the dataset is not ridden.
Nov 22, 2021 Very easy Other practical tools.
Nov 22, 2021 It is very simple and understandable add an image of where to locate "See all histories"
Nov 22, 2021 Lo amigable del programa Incluir la aplicación de cada herramienta usada
Nov 21, 2021 The webpage is friendly This is my first time on platform, so I need to explore more
Nov 21, 2021 That goes step by step, shows and explains each section Give an example of where we can obtain the sequences or which links are the ones that can be used.
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Mar 31, 2022 not that much reduce unnecessary details from the page
Oct 22, 2021 Explanation is naïve Importing the iris workflow is generating error while making plot. Have a look on it.

Metabolomics

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Oct 14, 2020 Well explained and simple to follow Include a workflow for GCMS analysis
Oct 30, 2019 Comprehensive in terms of breadth; hands-on
Sep 29, 2019 All the careful and detailed explanations make the training easy to follow
Sep 18, 2019 The detailed explanation behind the steps. It was awesome
Jul 6, 2019 This format is much more approachable (esp. for hands-on) than the PDFs at W4M.org. I'm not saying that the PDFs are not helpful or informative (they are), but this is much more suitable for walking through the steps. Also, because it is a "living document", you can improve it in place, and we do not need to look for an updated document somewhere else. We can always link to one URL when referencing the tutorial. Document every axis of every panel of Quality_Metrics_figure.pdf, e.g., what are deciles and missing values in the bottom left panel? Put into the description the rationale behind the parameters chosen in Data Filtering (you presented it wonderfully verbally, but I don't find it written into the tutorial).
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Mar 30, 2022 Imaging and locating the capscicin
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Feb 8, 2022 easy workflow The metaMS.plot does not work

Metagenomics

85 responses
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Aug 4, 2022 It was explained in really easy to understand language for a novice like me with great diagrams. I've looked at a number of explanations about alpha and beta diversity and this was the most useful so far.
Jun 24, 2022 The clarity and flow of topics guidelines so far so good
Jun 24, 2022 Well-detailed Alphadiversity
Apr 13, 2022 Each step of the analysis is very well explained and I could use this tutorial to help student understand 16S microbiome analysis. The trainsets need updating. I tried to do this myself but it did not work. Also, could you do a version for ITS analysis?
Mar 21, 2022 nothing nothing
Mar 21, 2022 nothing everything
Jul 17, 2021 Awesome! Thanks a lot
Feb 19, 2021 Very informative yet concise. Did an excellent job of walking through the parameters needed for each step. Also appreciated the walking through of visualization and statistical significance rather than ending at the OTU clustering.
Jan 7, 2021 The explaination about each step
Aug 29, 2020 Absolutamente todo. Cada sección perfectamente bien ejemplificado con teoría
Jun 9, 2020 Very interactive and gave detailed instructions about what to do and why. Very beginner friendly Give brief introduction about the files extensions (for example what is a FASTQ/FASTA file?)
May 12, 2020 it is hands on course I did not understand meaning of many options.
Apr 9, 2020 The fact that there was an exlpanation on why we are doing all these steps Maybe adding PCA
Feb 14, 2020 It was quite easy to follow and understand I saw 0.31 instead of 0.03 in the cut off box several times, would be better if it is corrected to 0.03 which is equal to 97%
Dec 30, 2019 I liked the step-by-step how to instructions I got lost at "make.contigs" - could not find out how to use that tool in Galaxy :(
Oct 2, 2019 Perfectly explained The use of the Venn software was not available
Sep 5, 2019
Aug 2, 2019 The mouse.dpw.metadata is not in the downloads at start nor linked at bottom. Please add to tutorial.
May 3, 2019 easy step by step guide to analysing 16s rRNA data When you say skip mock test if time retrain, skip whole section to OTU step? More information of the choice of databases used and do we use all etc?
Apr 24, 2019 Everything
Mar 12, 2019 Clear explanations of the tools; helpful workflow; I think the Hand On opportunities and prompt questions are really beneficial. Descriptions of which files to use were not always clear enough for me to determine which one to use. The justification of some selections for tool options could be expanded on, or additional links to papers noted where appropriate.
Mar 10, 2019 that it went right from the beginning (fastq) with explanations at each point of what I was looking at the galaxy biom1 file output does not open successfully in Phinch, preventing the final visualisation
Mar 9, 2019 Step-by-step guidance to complete tutorial, comprehensive and easy to understand and follow along
Oct 19, 2018 Clarity and background details Need a step on how to remove barcodes, adapters and primers from raw FASTAq sequences
Sep 17, 2018 The data clean-up was thoroughly covered. Every step was well explained Using the mock community. More light on rationale
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Nov 2, 2022 Hands in Videos might help us more
May 17, 2022 Simplicity of explaining complicate issue (-; n.a.
Jul 11, 2020 well described help when stuck
Dec 29, 2019 flow of the tutorial more accurate galaxy functions reference.
Apr 13, 2019 step by step very well described data analysis with OTU / phylotype
Nov 14, 2018 clear step by step module
Nov 14, 2018 The overview of all the tools available. The time for the processes on Galaxy.
Oct 30, 2018 Some instructions were not clear at all, please be more specific as i encounter errors very likely despite following the steps Please review the protocol and revise some segments
Oct 29, 2018 Krona It needs to be updated, some returns error and some is missing. Be more detail and specific
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Mar 21, 2022 the training used different tools and explained how each works as compared to other tolls
Mar 16, 2022 As someone working on AMR, it was really interesting
Dec 5, 2020 User-friendly /
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Mar 30, 2022 I WAS NOT AWARE THE OPTION WHERE YOU CAN GROUP YOUR DATA AND ANALYZE IT AS A COLLECTION, THANKS A LOT
Mar 29, 2022 the pace and amount of information was just right, very clear and understandable :)
Mar 16, 2022 great tutorial, very well explained
Dec 5, 2021 Stepwise, just in time learning and great links to additional information (Having the video helped), but the steps were all included.
Aug 2, 2019 The Krona plot - this appears to be of all samples. Would be good to per sample. Might not be possible with Phinch. As for Phinch, that is no longer web accessible but standalone and has dropped functionality.
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Nov 10, 2021 Yes
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Mar 16, 2022 great tutorial
Oct 16, 2021 Clarity Please add Bracken
Feb 17, 2021 Complete pipeline to analyse nanopore data. Easy tutorial and results are very clear with a visualisation with krona
Dec 18, 2020 easy to follow, well explained more insight on the different options
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Mar 18, 2022 Great workflow ! I have done this on the CLI... only installing humann took a while! It's great that this workflow can be used by biologists

Proteomics

49 responses
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Sep 8, 2021 Very well explained
May 22, 2020 Extremely clear and easy to follow Maybe add the subheadings in the tool library under which the specific tools can be found
Sep 29, 2018 Many details and background information Fasta merging parameter How are sequences judged to be unique? should be set to 'Accession only'
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Sep 29, 2018 Well explained, great background information - my favourite was the greedy group resolution
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Dec 5, 2018 Tutorial is absolutely awesome! Thaks a lot for the work you made! Maybe you could make the tutorial more detailed. Write all the commands exactly as they should be written in the terminal. I catch lots of failures and can't improve them by myself.(
Oct 3, 2018 Background info such as: The explanation of 'doubtful' for all levels SearchGui crashed with the database containing mycoplasma, with human and crap database it worked
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Apr 26, 2019 still to complex to make sense
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Aug 14, 2021 short but precise information about technique little bit more information about difference in data analysis part of labelled vs label-free methods.
Mar 26, 2021 Brief description of key issues
Mar 2, 2020 very detailed
Jun 1, 2019 Detailed of both technique are very concise and helpful
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Mar 18, 2022 Basics explained and accessible, which can be improved to acquire advanced skills and knowledge. thanks.
Sep 11, 2021 Really clear
Apr 6, 2021 really detailed and clear! some tools have different names (e.g. it's now 'Pathway enrichment analysis [Reactome]' instead of 'Query pathway database [Reactome]', I think; in other words I couldn't find 'Query pathway database [Reactome]' so I improvised with 'Pathway enrichment analysis [Reactome]'). Also it would be good to include some tools to analise data other than these 3 species.
Nov 24, 2020 I couldn't get past the "filter" part of this exercise because it did not explicitly state what filter tool to use. Filter using what? Again, many of your modules are helpful, but just as many need a biologist that is not a bioinformatics expert to help you understand where your directions are not clear. This module seems to have been edited by people that know bioinformatics, so all the stuff that's obvious to them isn't caught.
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Jul 19, 2022 The step by step guide and easy to operate I facet some trouble with Database/Build section and I would like to info about them even it was not necessary for the analyse.
Aug 23, 2021 Well described steps for analysis of proteomic data Include statistical analysis methods
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Mar 19, 2022 very interesting tutorial
Mar 17, 2022 very complex biological/ bioinfo problem solved thanks to this great workflow. available and accessible to the whole of the scientific community. Great! Thanks for all contributors and participants.
Feb 18, 2021 very clear descriptions of all steps
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Mar 20, 2022 very useful pipeline
Mar 17, 2022 very complex biological/ bioinfo problem solved thanks to this great workflow. available and accessible to the whole of the scientific community. Great! Thanks for all contributors and participants.
Feb 19, 2021 The presentation was great: first the explanantion what we will do and why, and then tutorial.
Feb 18, 2021 clear and concise descriptions of each step provide all necessary input files from tutorial 1 on zenodo
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Mar 17, 2022 very complex biological/ bioinfo problem solved thanks to this great workflow. available and accessible to the whole of the scientific community. Great! Thanks for all contributors and participants of the GalaxyP
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Jul 18, 2021 How can we use/apply this successful models to our real cases/samples?
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Mar 16, 2022 Great introduction to proteomics tools
Jul 26, 2021 the interactive tools the tools were difficult to find. please mention the tools very specifically in the tutorial
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Jun 7, 2022 The questions that helped you look for the most relevant information in each Galaxy output in the history really made the tutorial engaging.
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Aug 22, 2022 The flow and easeness of usage and details.
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Sequence analysis

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May 15, 2022 yes
Apr 17, 2022 It was good and simple. More indications on how to read the visualization with IGV and JBrowse.
Mar 17, 2022 compact and fully covering the matter, thanks
Mar 17, 2022 clearly and easily explained. very good, many thanks Maybe more details in the video for the advanced, but all is mostly available on this web site. thanks.
Mar 17, 2022 The tutorial was informative. Visualizing the reads in IGV (as a WSL user) was great.
Mar 16, 2022 Easy to follow
Mar 16, 2022 how to do read mapping and understanding the statistics
Mar 15, 2022 The IGV tutorial was great
Mar 15, 2022 I struggled to access the built-in reference genome and ended up giving up on the tutorial
Mar 15, 2022 very informative
Mar 15, 2022 that we could do things side by side to the instructor it could be more interactive
Feb 25, 2022 The clear explanation of the tools
Aug 11, 2021 The tutorial is very helpful
Aug 11, 2021 Explanation of the steps Nothing
Aug 10, 2021 The combination of both theoretical concepts and practicals.
Aug 10, 2021 Easy to read instructions, easy to find tools The IGV output information. What the colours mean actually, what info can I extract from there. More step-by-step guide what and how can i visualize for the most info. Maybe some tasks what to search for.
Jul 9, 2021 Easy to follow with concise description at each step. The IGV browser to browse the alignment was just out of the understanding. I personally didn't understand anything how to read it, how to visualize it and extract useful data, why only visualized chr2 and not the others? What info did we get from visualizing it.
Apr 22, 2021 The solutions after each question Te previous tutorial (quality control) was more easy to follow the different steps
Feb 16, 2021 The tutorial was easy to follow. There are very many different choices to make - a fold-out in the tutorial of just some of themwould be nice.
Feb 15, 2021 Very clear and interesting. IGV and JBrowse are indeed very interesting tools to view alignment !
Apr 8, 2020 Easy to follow for beginners Need more information about non default setting of Bowtie2 and SAMtools
Jan 8, 2020 It was largely well-written. The JBrowse tool would not show me anything in that bit of the chromosome and kept erroring 'name can't be found'
Jul 18, 2019 Almost everything In step 1 of "Hands-on: Mapping with Bowtie2" your instructions mention that the paired-end input is the output of Trim Galore!. However, the previous tutorial on quality control uses MultiQC. As such, the reader of this tutorial will be confused. In "Hands on-Inspect a BAM/SAM file" the 11 fields listed in the tutorial (QNAME, FLAG...) do not match with the 10 field names in the output produced (QNAME, FLAG, RNAME, POS, MAPQ, CIGAR, MRNM, MPOS, ISIZE, SEQ). The JBrowse viewer, doesn't work for me, get an error
Jul 15, 2019 Very clear instructions More details on the Selection of analysis mode (non default option)
Sep 17, 2018 Very detailed, thank you
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Oct 31, 2022 The video walkthrough of how to use tools was good. Breakdown of sections with a Table of Contents to jump around was good. I like that extra detail was included, but it's so far above my head I didn't understand those at all. Thanks for the wonderful visuals, it really helps explain the relevance of each section. The beginning of the webpage and the tutorial video was actually very clear and easy to understand, it gets a bit more convoluted about halfway through and really by the end before the Nanoplot stuff (video ends before that). I would have preferred if additional visual aids were used instead of just a plain screen grab. Some of the text was hard to read even on a large TV screen. Highlighting or circling or arrows, anything would help to focus the viewer's attention towards the relevant topic area. Some written aids which could be directly taken from the written webpage might be handy to sync up reading the webpage and following along with the tutorial would be nice for newbie readers who don't actually understand what's going on. An example would be just titling the section with big obvious words that match the webpage's Table of Content. And useful on screen aids like showing the buttons for pressing and holding Control OR Command with the symbols would be helpful for those following along. That's not a thing that can be demonstrated on the screen itself and can easily be overlooked as it's only mentioned for a few seconds. Then the important changes from FASTQC to MULTIQC where you must change the file input from a single file to multiple files, that right there would benefit from circling or highlighting or drawing a box around that button, maybe zooming in too. It doesn't need to be fancy Hollywood graphics here. The same video can still be used but for those few seconds that he's saying what button to press, you could use a screenshot, recorded in Powerpoint in Presentation mode with nice transitions, use the Zoom effect for each area like typing into the Upload Data section, draw a box around that button, then the Zoom back out transition to the MULTIQC options, draw a box on the button for multiple file uploads, Zoom in or out, up to you there, then return to the original video footage. I know it's simplistic, but it helps alot for new users instead of overwhelming them with a 3 panel screen with a billion options. It would be nice if this page could easily have a printout to save as PDF and have an option for all the solution and detail boxes to either by opened or closed (useful for writing notes and testing myself before seeing the answers. It would also be nice to have details be a separate option from solutions). I think the presenter needs to name his files better. By the end of this, he was just referring to them as "the FASTQC file from step 17", by this point, as a newbie, I've screwed up so much, my order doesn't match his at all, I've deleted some steps, and re-run them, and the order continues incrementing, so nothing matches his and I have no idea if I'm selecting the right files or not. This video was really long. And I see sections that aren't included in the original for the Nanopore and long read stuff. Perhaps this would benefit from splitting the video into multiple different videos? Or adding chapters to the current one at least? Chapters corresponding to the Table of Contents names of course. This way it would improve your Youtube video's SEO and usability for users who are probably having multiple sessions watching this spread out over hours anyway. Although I think the better approach for easy future re-recording would be to split it into smaller video sections based on each Table of Contents entry. I don't see why the videos can't be directly embedded on this Training Galaxy page either, right at the top of each titled section. I think there are too many assumptions that people should know why something should be good or bad or high or low. Even as someone with a Biology background, I haven't delved deeply into sequencing reads before and don't know how to interpret this. It would be helpful to add something like what Phoronix does for benchmarking charts with a directional arrow indicating which way is better: https://www.phoronix.com/review/amd-ryzen7-6850u/8 and I suppose it could be added as video tutorial visuals or as just a labelled screenshot. My Nanoplot attempt had an error. It would be nice if you had a built-in automated bug reporting button, either in Galaxy, or in your tutorial or just the link or wherever. Just put it somewhere and make it 100% automated so that the user doesn't need to try to figure it out. Make it somehow able to click at the step of the tutorial or report the link as broken or the results as broken. I don't get an HTML page, and I don't know why. It's a bunch of HTML code so I can tell it SHOULD BE an HTML page and the History says so, but trying to download it to read and trying to open it in Galaxy doesn't work. On a related note, some of the buttons have changed, I think even the datasets have changed and don't match what the tutorial video shows. It would be nice if you had an updated one that matched.
Sep 5, 2022 I really liked the amount of details Its perfect to me, but if you could add short videos in each topic, it can be complementary.
Sep 1, 2022 Learn about other tools to asses quality, it is often on software that we use, the one that is showed by the person that initiates us to galaxy. Here, we could see a panel of tools. I think maybe it is more pertinent to show one example of good and one of a bad data instead of a panel that increase the information a blur the message. Two images are easier to remember. I'd like that you showed us a panel of tools, but it is maybe too much information, too quickly within a short amount of time. Knowing that we have almost two weeks formations non stop, it could be valuable to synthesis more the message to slow down and make it more digestible. The specifics could be prospected by each user when they contact you. A fact that you could also remember people at the end of the presentation.
Aug 11, 2022 Things are explained in a simple and intuitive way
Jul 11, 2022 it was information packed and tried to explain in details. well , idk if i'm dumb but i couldn't find the gear icon to start the ctul tutorial. maybe the boxes in the instruction could be direct links instead?
Jun 29, 2022 Very detailed, self explanatory More examples maybe good
Jun 28, 2022 easy to follow & explained well
Jun 7, 2022 Well organized. Appreciated how the authors explained each QC graph.
May 4, 2022 Its simplicity. It was easy to follow and didn't make me stressed.
Apr 4, 2022 EVERYTHING NOTHING
Mar 31, 2022 give pictures like other tutorial
Mar 29, 2022 Getting to run data through Galaxy Maybe more schemes to describe the reads for the relevant platform
Mar 29, 2022 it was okay everything is perfect
Mar 16, 2022 It was my first time analyzing the quality of a sequencing experiment and I easily followed the tutorial. This mean to me that it was nicely prepare taking care of the details.
Mar 15, 2022 learned new QC checking tools, I only knew fastQC great tutorial
Mar 15, 2022 I was already familiar with fastqc, but learning about Nanoplot and PycoQC for long read quality control was great
Mar 15, 2022 Really liked the given details about each quality parameter
Mar 15, 2022 great tutorial on the basics ! nothing
Mar 15, 2022 that the work can be excecated at the same time the class is on if we could question the instructor
Mar 15, 2022
Dec 8, 2021 The course is elaborated with proper hands on help and graphical representation. Its gives proper details for each and every concept.
Nov 10, 2021 Graphics Putting animations and explanatory videos
Nov 8, 2021 easy tasks, everything worked
Nov 7, 2021 i understand better quality control of the data more examples or more quiz examples
Nov 2, 2021 Explications More videos
Oct 31, 2021 The hands on part Add a video
Oct 27, 2021 it was really great and very informative tutorial, documintation and blasting over represnted sequences , made me feel getting on more with the tools and the data the part which talks about the best alingment algorithm for adapters was not very clear for me
Oct 1, 2021 great including other QC parameters as well
Aug 19, 2021 the brief explanation of each step
Aug 18, 2021 The way you collect all the necessary info including the definition of each step and the examples of errors Optional document for other examples of the bad quality data with more clear explanation
Aug 14, 2021 training is great
Aug 12, 2021 your explanation of each plaot
Aug 12, 2021 The details
Aug 12, 2021 Everything None
Aug 11, 2021 Simple steps and result interpretation/ detailing in each steps. Frequently asked questions inclusion would help. Link doesnot work
Aug 10, 2021 Easy to follow Not much, overall superb
Aug 10, 2021 It presents both the theoretical concept and practical aspects simultaneously
Jul 29, 2021 It was fairly clear Did not discuss removing duplicates from raw reads. Also the formatting of the options in a line of code was not super easy to read. Maybe after explaining each parameter, also show an example of it all in the same line together.
Jul 16, 2021 very good explanation nothing
Jul 8, 2021 The simple to follow tutorial and best of all, the description given at each step. It's concise and extremely helpful. Not all of the parameters in the report generated by MultiQC are discussed. I think, a few lines about each of them will do great.
Jul 1, 2021 everything with your YouTube channel guidance it difficult to understand in the beginning so also mention your link here too.
Jun 27, 2021 The explanations were easy to understand while explaining the intuition behind the graphs and the quality of the data. The sound has sudden drops and highs making it hard to follow at specific points.
Jun 22, 2021 Clear explanation about QC reports Adaptor trimming
May 31, 2021 Step by step process and questions to think about Maybe screenshots of selections
Apr 24, 2021 the detail in the explanations, the examples included
Feb 27, 2021 Clear and easy to follow, and tones of additional information. More images perhaps
Feb 18, 2021 Very clear and helpful for first time users
Feb 17, 2021 It was very straight forward with clear language and explanations. I found it both very detailed and somehow concise and palatable. nothing at all at the moment.
Feb 17, 2021 very clear instructions, step by step to go back and repeat if need to do not sure, but also following the video to complement the instructions was great
Feb 16, 2021 Everything about the lesson was crisp in explanation and content I believe the tutorial is next to perfect
Feb 16, 2021 Very easy to follow
Feb 15, 2021 It was clear and easy to follow.
Feb 15, 2021 Very clear, all tools are clearly explained, small questions to help us understand the output results
Dec 30, 2020 It is very complet. It could be said some points that are on Galaxy (the 'Yes/No' parts) and are not fully explained.
Nov 19, 2020 Clear and easy to follow
Nov 18, 2020 That it is hands-on and with detailed explenations
Nov 18, 2020 Easy to follow an sufficient information at each step. The WEB-output of the MultiQC did not work. I don't know if this is a Galaxy-issue or some lacking information in the tutorial?
Oct 1, 2020 The really clear explanation of everything!
Sep 29, 2020 Straightforward tutorial
Jul 26, 2020 Part from read quality You can give more detailed explanation of each module with appropriate reason and example in assessing read quality part.
May 20, 2020 Clarity
May 18, 2020 I liked examples that I could use for practice. I would like to see more information about adapter detection and removal.
Apr 15, 2020 I liked to explain the steps thank you I think everything was good for me. But I gave you 4-on-5 because I had a hard time applying the last two phases.
Apr 9, 2020 The tutorial is clear and easy to be understand everything is great :)
Mar 26, 2020 That I can get extra info about some of the things, but it is not included in the main scope of the tutorial (the grey info boxes). For my purpose right now, I want to read it, so I am gratefull it is there. But I also sometimes check manuals where I don't need to know everything, but just get my analysis to work
Jan 13, 2020 It is very interesting tutorial
Jan 7, 2020 It was so clearly divided up. I loved the different icons/open/close boxes that made things make so much sense AND could show main points & extra info. It's hard as an outsider to understand priorities, so that was brilliant.
Nov 20, 2019 why not using trim galore instead of cutadapt?
Oct 11, 2019 Easy to follow Not much really
Oct 7, 2019 Overall, the manual and following the course was good. More explanation and better voice quality.
Oct 7, 2019 Materials are well crafted. Sound issues. Need of a better microphone? Could also be the speakers in Estonia.
Oct 7, 2019 I like that there is a lot of info and examples.
Oct 7, 2019 Tutorial is very detailed and clear
Oct 7, 2019 simplicity of the tutorial explain more the available options of each menu and the biological meaning of each choice
Oct 7, 2019 Good overview of the principle To show more of the bad quality examples
Oct 7, 2019 The available paremeters per step should be more elaborated in order to understand how we can use them in other context and queries
Sep 24, 2019 Good advices by the teacher to understand the workflow
Sep 14, 2019 really helpful for first timers using fastqc, thank you. provide images of what the results should look like. Also, there are a few typos like 'how many basepairs has been removed' instead of 'how many base-pairs have been removed'
Aug 23, 2019 The material Figuring out why the mapping tutorial directed me here to quality control fastq files then they will not work...
Aug 21, 2019 Easy to follow steps Considering SNP in the analysis, practice adapters removal ?
Jul 27, 2019 step by step instruction don't know
Jul 18, 2019 Step-by-step instructions and showing results. Questions to test understanding.
Jul 17, 2019 Amost everything! In your tutorial, you state "In this training, no adapters were already removed". What does this mean? That adapters were not removed? Then why do we not remove them in the tutorial? From a grammatical point of view your sentence is confusing. Do you mean "In this training, adapters were not yet removed"?
Jul 15, 2019 Very Clear and well-thought instructions. Appreciated effort
May 14, 2019 solid logic and small amount of valuable information Probably as we are not trimming any adaptors in this tutorial, Trimmomatic can also be used on datasets provided.
Mar 20, 2019 very clear specificity of quality check regarding the type of data (16S, whole genome)
Dec 10, 2018 Nice explanation, really easy! what is the next step?
Oct 31, 2018 all of it! how to rmemeber steps....
Oct 8, 2018 Examples and questionaries with solutions :-) More details regarding others output sections of FastQC tool
Sep 22, 2018 Not clear that Trim Galore and FastQ are integrated into Galaxy. Uncertain how obtained 97,644 sequences after trim galore of bad data (I got 99,341).
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Aug 11, 2021 The mapping part was very interesting. More examples to explain the concept would do better.
Aug 11, 2021 The activity is very interactive.

Statistics and machine learning

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Oct 13, 2020 It was very clear Yes: some of the parameters are not mentioned (whether we should change them or leave by default). All not mentioned parameters I left by default, but I am not sure it is right.
Jul 6, 2020 Very good examples I don't know anything about ML and I started with this tutorial (because it's the first lesson) and I think it is more complicated than the following ones, maybe it could be a future Lesson. I also have problems understanding about pipelines, but it could be me
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Oct 9, 2021 simple enough to follow It would be nice if a bit more background of machine learning is described.
Dec 23, 2020 concise, clear fast to perform
Apr 25, 2020 Strict, explicit instructions on what settings to enter into which category, leaving no room for ambiguity. Specifying where exactly to find "Support vector machines (SVMs) for classification". This entry shows up both under Statistics and Machine Learning, and with no immediate indication of which one to use - likely because they're both the same tool.
Jul 6, 2019 Easy way to use machine learning maybe more information or link for understand each advanced parameters
Mar 18, 2019 This was a helpful example for how machine learning can be applied to a real-world dataset. Add more info on how to access the SVM Classifier tool. This tool does not seem to be available in the US Galaxy instance, but it is available in the EU Galaxy instance.
Mar 8, 2019 very straightforward tutorial
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Sep 2, 2019 Short and efficient primer The theory behind the method in this particular example could be more expanded
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Feb 18, 2021 Very easy and simple to understand
Apr 25, 2020 Exhaustive and extensive introductory chapter, easing readers into complex concepts without the need for in-depth prior knowledge. The English used in the introductory section is spotty, containing grammatical errors and incorrect use of prepositions in many places. It misattributes terminology to mathematics when said terms more properly belong to neural networks or programming. The text contains types, such as Figure 1 being referred to as Figure 3 in at least one place.
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Jun 18, 2021 very intuitive everything is great
Jul 9, 2020 very good examples, easy to follow
Jun 26, 2020 Self-explanatory well structured instructions The applications of these methods on life science large datasets
Jun 26, 2020 Easy instructions, good interpretation More interpretation
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Mar 22, 2022 excellent content overall loved it
Oct 26, 2020 It analyzes biological data in a user-friendly platform. Giving more examples of biological data.
Oct 26, 2020 Simplicity and explanation Idk
Oct 26, 2020 To get to know Galaxy tools You could make breakout rooms to catch up between steps.
Oct 26, 2020 It is very well organized More information links for each parameter could be provided. I did the tutorial in a one-day lesson I did not get the concepts of each parameter.
Oct 26, 2020 the reproducibility a better way to find the tools
Jun 24, 2020 In one place you write: “Select input data file”: test_rows_labels_without_header.csv Here the ".csv" suffix is not needed because it's not part of the name we gave to it. It's tabular file anyway. In multiple places the figure references are wrong: The residual plot shown in figure 9 -> figure 7 To infer how its values exhibit model performance, we can compare the figures 7 and 8. -> figures 8 and 9 Figures 5, 6 and 9 show that the prediction is acceptable -> figures 5, 6 and 7 The idea of cross-validation is shown in figure 3. -> figure 12
Jun 23, 2020 Clarity and detail. Nothing I can think of...
Jun 23, 2020 The description of each step is really clear. In the end the "key points" is also good.
Jun 23, 2020 It's nice that the output plots are shown and some parts/questions are hidden and you just need to open them if you dont know. At the beginning, all files are renamed which helps to follow the tutorial, but later on, this parts are being skipped and you can get lost it is very bad to find the tools for first use. the search box is not working properly. I know its a galaxy problem, but you should state in the tutorial were to find the tools!
Jun 23, 2020 clear self-explanatory steps for execution N.A
Jun 20, 2020 Tutorial steps are different in the latest Galaxy and should take a review
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Mar 22, 2022 Amazing tutorial overall
Jul 18, 2020 The tutorial was very clear and well-structured. Include a second dataset with "bad" data in order to contrast when the classifier worked or failed
Jul 7, 2020 Amazing, easy to follow and very usefull examples of the differents ML models
Jun 25, 2020 20 - even though the default value of the number of estimators for Bagging Classifier is 10, 20 gives the best accuracy. Not for me. Both 50 and 10 have better results for me. I guess because we did not set a random seed. "Now, we will predict age in the test dataset using this model." "Hands-on: Predict age" This is copy&paste from the regression tutorial. Actually we are predicting if the molecules are biodegradable. "Figure 13 shows that we again achieved an AUC value of 1.00" That's figure 12.
Jun 25, 2020 The explanation and description are easy to follow and understand. It would be better if all the evaluation plots of different models (e.g. Confusion matrix) were put together. Then it's easier to have an overview of performances.
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Jul 14, 2021 Hi, unfortunately, this tutorial will only be useful to those who already know the method. As non-bioinformatician, I have no clue what this is good for. Can I do GWAS with that and how do I implement it? Such tutorials should be cross-checked by biologists, bioinformaticians can solve such problems anyway themselves.
Nov 24, 2020 Use of images and screenshots helps guide the training process, as users know what to look for. Explanatory text needs to be substantially expanded, explaining what Interval-Wise Testing is at least in layman's terms. Additionally, explanations for data shown in images is required, else these images appear meaningless. IWT is not well-known enough to leave these things assumed.
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Mar 31, 2022 great tutorial overall
Dec 8, 2021 this tutorial explains CNN for image analysis completely and simply.
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Mar 30, 2022 very interesting tutorial overall
Mar 12, 2022 simplicity
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Jul 1, 2022 The way of presentation to make the tutorial easily understandable. More numerical examples could be added.
Mar 31, 2022 Simple and concise
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Mar 31, 2022 great overall
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Aug 4, 2022 Great overview of ML and the basic models to start. Many questions still lack solutions and there are some typos within the text.
Jun 2, 2022 I liked the real world data set, and the real world steps of exploration followed by the analysis. I thought the step wise progression made a lot of sense to me. I like having both predicting a categorical variable and the linear regression. It was great having both as many tutorials concentrate on predicting dichotomous outcomes and skip linear. I also like the exposure to handy R libraries, I am aware of quite a few (this isn't my first rodeo) but I learned of some more from this tutorial which was great. Perhaps be explicit about the goals for the data analysis of the breast cancer dataset, that way the reader gets emotionally engaged in the analysis. I didn't realise till after looking at the source link that the measurements were from fine-needle biopsies of breast lesions, and the measurements were of cell nucleus radius, (I thought originally it might have been referring to tumour radius in mm). And that the goals were from the cell data from the fine needle aspiration we need to predict whether the patient has breast cancer or not. I appreciate you don't want the tutorial to be too long but perhaps using the cross table to show the positive predictive value or sensitivity and specificity and how increasing the number of clusters could improve the diagnostic accuracy.
May 11, 2022 Easy to understand Pls provide dataset so that we can practice alongside

Teaching and Hosting Galaxy training

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Apr 29, 2022 The stages of preparing a workshop is very explicit on . Thanks. The processes are clear.and direct.

Transcriptomics

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Nov 9, 2022 Very comprehensive and detailed This is already so awesome but If possible could you please add along with this tutorial the pipeline/command line that could be run on MacOS terminal? We would be very appreciate that. Many Thanks!!!
Aug 18, 2022 Small typo at https://bit.ly/3dG17Er - tedious
Jul 19, 2022 It was easy to follow and very useful
Apr 26, 2022 The tutorial is very comprehensive. The link for the Ensembl gene annotation for Drosophila melanogaster from Zenodo doesn't work. I think there are mistakes regarding the datasets and tools to be used in the "Gene Ontology analysis" section, more precisely in the "Hands on: Get the gene length from previous history" and "Hands on: Adapt the gene length to goseq" parts.
Apr 11, 2022 great explanation
Mar 27, 2022 The extensive description I think that it is helpful to be conducted by the instructors and the extra practice which there are in the solutions for the questions because in some parts there is confusion.
Mar 27, 2022 This is the most extensive and instructive tutorial I've ever taken on Galaxy. My understanding of RNA-seq and DGE analysis has been improved greatly. I made some mistakes along the way which prevented certain analyses from working, but I learnt from them.
Mar 19, 2022 All over the presentation is nice and each steps are clearly explained. Sometimes the tools are not appeared during performing a search and sometimes other tools are also appeared. It will be better if only relevant tools can be found with the keywords for a specific type of data analysis.
Mar 18, 2022 The tutorial is super clear and easy to follow
Jul 21, 2021 Detail explanation of process from A to Z. Maybe adding some more of data interpretation/graph interpretation. Even without this, Tutorial is great. Thank you so much for your hard work and the dedication you put on this tutorial.
Jul 8, 2021 Explaination and discussions on quizes
Jul 6, 2021 very clear steps and hands-on instruction some tools used in the tutorial have namesake with different function, for example, tool "cut" have two versions, but function is different.
Jul 1, 2021 some tools connect to different tools, like cut that goes to advanced cut
Jun 5, 2021 The details that were explained are hard to get elsewhere and they were explained in a very lucid and uncomplicated manner that made it a pleasure to read on Perhaps a more detailed conclusion about the final results obtained in a paragraph style will be the best way to end the discussion.
Feb 21, 2021 So useful from getting the data to pathway analysis!!
Feb 19, 2021 The steps were very clear Make a tutorial for miRNAs in humans
Feb 19, 2021 The clarity and order of the explanation
Feb 17, 2021 Very good level of detail. Just appropriate.
Feb 16, 2021 Very clear explanation. Video makes it easier to understand results. The small questions are very good, helps to better understand results. Functional enrichment of DEGs was very interesting with clear visualization.
Feb 15, 2021 The detail and complexity. Fantastic! Possibly broken into smaller tutorials?
Nov 24, 2020 I wonder if you have considered asking biologists that are not trained in bioinformatics to go through your materials. There's a fair bit of shorthand and lack of clarity in this module that leads me to believe skilled bioinformaticians are editing this material for clarity (and therefore thinking that it's clearly written because it's clear to them). If true, this seems to defy the mission of making the module learnable by non-bioinformaticians. Many of your modules are clear and I enjoy them, but it's unfortunate that this one is not as clear.
Nov 22, 2020 easy to follow yet very comprehensive its perfect
Nov 5, 2020 explain single parameters in the tools more
Nov 5, 2020 RNA Star failed to generate output files in the mapping step. I think it might be because Drosophila_melanogaster.BDGP6.87.gtf was not recognized as a gtf file. Even if I manually assigned the gtf format while I was uploading it, the uploaded version showed warning in the expanded section indicating that the file is not recognized as gtf.
May 25, 2020 straight forward easy to follow
Oct 22, 2019 Each step is very detailed Provide a video or screenshot
Oct 20, 2019 It is a perfect introduction!
Oct 8, 2019 Good materials. Good clear presentations. The tempo in the afternoon session was at times too fast. The tools are slow and at least I was lagging behind at some points. The presentation on general RNA sequencing could maybe fit better after general Galaxy presentation, which took place yesterday. It would be more engaging if the presentation was tied to some kind of real experiment. e.g. we are trying to find out what happens after some treatment and we reach a conclusion afterwards.
Oct 8, 2019 Got a good basic overview of the workflow One needs just more time to dive into the different parts of presented analysis..
Oct 8, 2019 very useful topics it was a bit tiring at the end, where the most valuable things were taught
Oct 8, 2019 detailed explanation of all the options that can be altered in each tool
Sep 25, 2019 Everything. Use of a google doc for people who are shy was very thoughtful. I have rarely seen such care by organisers. Thank you very much! Some links with video recording of a person performing the tutorial while explaining the steps and variations that can be performed. It will be a very useful for people who cannot afford to attend the workshop. Sorry for suggesting more work. But you are so close to a perfect tutorial. Thanks again!
Sep 25, 2019 I liked that it is very detailed, easy to follow. The only moment when I was lost was where to find Galaxy Upload Manager (maybe an icon shown in tutorial will be helpful?). It is a lot of information everyday during the tutorial, short summaries after each step (maybe with writing big steps on the white board) could improve the training even more.
Sep 25, 2019 I liked that the tools we've learned today were very practical ande represented entire workflow for data analysis from the moment we get fastq file from sequencing until the moment of data visualisation I would be nice to have a little more explanations of what certain parameters we set mean
Sep 25, 2019 very detailed explanation of the individual tools. the shared google docs file was actually very helpful to ask quastions in between
Sep 25, 2019 Did we learned how to visualize data on our own and we could write questions to you
Aug 28, 2019 Answers provided all along the tutorial to make sure we are correct when performing the tutorial alone Comment section to help people with trouble on this tutorial ?
Aug 9, 2019 There might be a bug in one of the tool form values. Search for "transform my data" in the hands on and compare to this short Q&A at Galaxy Help ("Log2(value)" in tuto versus "Log2(value+1) " when the user was given advice. I'll try to find time to test this, too, but anyone who gets there quicker wins the PR :) https://help.galaxyproject.org/t/fatal-error-heatmap2-tool/1288 The heatmap tool has been problematic on and off 6+ years. I'm not even sure if working at usegalaxy.org right now, or if at which, if any, other Galaxy servers. I stopped tracking it after it was broken for so long and just told people to use different tools. I'll review the MTS, etc... maybe some servers need an update. @jennaj
Aug 2, 2019 The easy step by step guide. It's good already!
Jun 12, 2019 You can work only on the tutorial and if you follow the descriptions carefully, you will get the result you expect to get. Explaining how to get the featureCounts data from another history (drag and drop and say it should be taken from another history in the first place).
Jun 12, 2019 waiting time during analyses
May 30, 2019 Clearly stated. I can not say for sure.
May 10, 2019 the "step by step "
Apr 12, 2019 Most complete tuto with lot of aspect. Maybe add so MULTIQC (for inferexperiment for example) for an easiest visualisation.
Jan 5, 2019 Nothing :) I think it's already good and clear as it is
Dec 3, 2018 step-by-step configuration colors to enhance instructions clarity
Oct 19, 2018 Topic and completeness of the scope I think there is an error: Join two Datasets tool * with (output of the last Filter tool) --> Should be with (output of Concatenate tool)
Sep 27, 2018 The tutorial was very interesting and easy to follow Naming of the output files
Sep 20, 2018 İts explanatory feature
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Nov 1, 2021 The overall design The fact that only one gene was differentially expressed means that there is a major problem with the data or analysis, and could not be used.
Sep 27, 2018 interesting and user friendly very good
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Oct 18, 2018 step by step manual it is good enough
Oct 18, 2018 Nice clear and good to start a bit further down for speed so it fits the program. note that the use of build list is unclear, perhaps good to move description of how to solve this up so to prevent questions.
Oct 18, 2018 Topic and clarity (DIY is easy)
Oct 18, 2018 It was well structured and simply explained It would be very helpful if the parameter setting on the tools was discussed a bit more and explain the reason why to certain choices
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Mar 19, 2022 An annotation part such as GO and KEGG pathway analysis should be included.
Nov 1, 2021 All the steps are fully documented and they always suggest further readings for important topics related to the tutorial. It is great to me, exactly how it is.
Aug 15, 2021 Maybe some more "solutions" along the way to help users check themselves for mistakes
Nov 6, 2019 Tutorial was technically speaking good, but wasn't matching the title Match the title... This was NOT "de-novo" Transcriptome-Assembly!!!
Feb 20, 2019 The explanation and description is easy to understand.
Dec 1, 2018 The explanations and solutions to check our output Explanations of the plots
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Nov 18, 2022 add the code of volcano plot
Oct 21, 2022 Ease of steps and explanation of file formats More explanation of the potential pitfalls and essential QC
May 18, 2022 The explanations
Mar 27, 2022 The ability to add labels on the volcano plot I think that this tutorial was very detailed, so it is not needed any improvement.
Mar 27, 2022 The tutorial was easy to follow
Mar 19, 2022 The way the instructor explained the plot and significance of it. It will be helpful if the steps to generate the input file limma-voome format using Galaxy tool is explained.
Jan 13, 2022 Clear instructions
Jul 31, 2021 very clear and to the point introduction to volcano plots links to what is Galaxy or galaxy introduction (I still have no idea what it is)
May 21, 2021 The graphs and Q&A Additional examples
Apr 12, 2021 the code
Nov 6, 2020 everything
Oct 23, 2020 Amazing! I was always afraid to get into R studio for the code needed to generate a Volcano Plot. So eaaasy here! I like it how it is
Aug 3, 2020 nothing no R code is available
May 18, 2020 For a biologist, getting a headstart in NGS analysis with user-friendly GI. Looking forward to learn more :) i like it so far. Everything was organised perfectly.
May 14, 2020 Well explained and simple to understand
Apr 20, 2020 The tutorial was very clear and straight to the point nothing
Apr 3, 2020 It was very clear!
Jun 20, 2019 complete, with examples (questions+solutions)
May 9, 2019 Tutorial doesn't have any public servers listed. Maybe a tool version conflict? Latest version is 0.0.3 and is installed at EU (and I made a request to add it to ORG). Are probably more tutorials like this -- seems the lists of "instances" is decreasing overall (bigger project, maybe good for the GTN or GCC co-fests)
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Jul 30, 2021 The clarity of the instructions. Great as it is.
Jul 23, 2021 Very hands-on! And the qc-report workflow can be directly used in furture
Jul 20, 2021 The step By step guide. adding videos for all the tuitorials as well
Mar 31, 2021 very friendly people and very informative. nothing
Mar 4, 2021 It is so clear to show the process step by step.
Sep 11, 2020 the clarity, and the examples
Sep 3, 2020 Very clear, easy to follow Examples with paired-end data, since there are additional complications
Jul 19, 2020 I liked that it was interactive and that there were datasets to apply to the exercises.
Apr 15, 2020 The workflow is very clear and easy to use A little bit more information about alternative parameters, like using other annotation files than the build in genome and going a bit further into the advanced parameters of the featurecounts tool (How to map per feature vs. metafeature)
Apr 5, 2020 Very clear tutorial thank you very much! :)
Mar 27, 2020 All There is a mistake in upload file . LF and LE are lactate luminal and not virgin luminal.
Dec 24, 2019 Stepwise procedure is helpful Additional GUI based support tool and environment , parameters like isoforms, splice variant, etc can also be explained in detail
Sep 16, 2019 very user friendly
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Jun 2, 2021 Quite clear overall There is no way to find out the p-values corresponding to the different colors, the meaning of the dotted and solid arrows, etc. Please add those information if you want to make your plots more comprehensible!
Jan 15, 2021 This tutorial would benefit from the addition of an updated data import section for the Zenodo inputs. Seems like a good candidate for a Co-Fest GTN+Papercuts contribution (should be quick to do + examples in other tutos). reminder @jennaj
Jul 23, 2020 exercises use data starting from scratch instead of already prepared data
Mar 10, 2020 easy to start and its not completely frustrating like the university slides. It's quite astonishing that our university can't provide clear instructions how stuff works but the platform that is aimed at scientists does a better job explaining it. Thanks a lot explanation part for hypergeometrical distribution is confusing me because the same words are used over and over again. maby include graphics to visualize the frequencies
Mar 28, 2019 Nicely explained and easy to follow even with own data. There is no explanation of the graph (colours, %, arrows) and meaning of columns in tabular output (Study#, pvalue, qvalue). Would be nice to shortly describe this with one example GO term.
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Mar 12, 2021 Thorough engagement with complex process of this analysis Some specifics: * No BAM to FastQ (used SamToFastq) * not clear what "the reference mRNA and TE fasta file" is * In "siRNA differential abundance testing" surely it should be Symp vs Blank? * Visualization section is missing * the miRNA reads are "removed for separate analysis" - what analysis is this? * Add some hats (this is hard!) I also resorted to writing some mini-workflows to make it easier to do some of the repetitive parts of the tutorial
Mar 25, 2020 the step by step approach take a look at the files, i could not find any adapters on the raw reads and therefore the "adapter trimming" section was hard to make. more explaination on what the different steps are good for, and why the three reference files (rRNA, miRNA_hairpin and transcriptome) are used in particular
May 20, 2019 Needs another step after "BAM-to-Fastq" is run. Tool outputs "fastq", not "fastqsanger". Redetecting the datatype will work. Other option is to modify the tool to try to assign "fastqsanger" (if the data matches that type, cannot be assume, I'll open an IUC request). See discussion/confusion from a tutorial user here: https://help.galaxyproject.org/t/convert-from-bam-to-fastq/1318
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Sep 17, 2021 Good explanation! Explanation on how to understand the figures in depth
Apr 28, 2021 easy to follow interactive plots could not be opened https://usegalaxy.org/datasets/bbd44e69cb8906b52089f52da217dea4/display/glimma_basalpregnant-basallactate/MD-Plot.html
Apr 14, 2021 I very much enjoy this tutorial! coming back from extensive R experience using limma, DEseq, still find this Galaxy thing makes things easier
Mar 31, 2021 It was really clear and easy to follow.
Aug 12, 2019 Easy to follow and showed what our plots/table should look like
Apr 18, 2019 Clear, comprehensive, great screenshots Nothing so far
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Dec 1, 2021 Everything! Very well organized and practical.
Dec 30, 2020 Easy to understand.
Oct 26, 2020 explanations easy to understand
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Dec 10, 2021 You iluustrated the principles of each analysis step. I am not sure where I can find the codes for practice.
Nov 4, 2021 This doesn't tell me what library or package heatmap2 function is in - i can't seem to find it elsewhere.
May 18, 2020 Detailed, organised and very easy to follow plus the additional questions and answers are good. It was good. More explanation on when to choose along with explanation of different options available in drop downs (but for this, the ones interested can go to links to figure out details too)
May 18, 2020 Every step is explained properly and easy to follow.
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Feb 8, 2022 It is very didactical a better explanation of cross-contamination plots
Aug 4, 2021 The variety of tools used. A clearer explanation about barcodes and batches.
Mar 11, 2021 All steps were clearly described and easily understood. I could not find the tool"filter bam dataset on a variety of attributes" in tool panel of Galaxy-human cell atlas , so I could not follow.
Jul 24, 2019 Clear step-by-step instructions Suggestions of what to do next once the count matrix has been constructed. Can one just use standard methods such as DESeq2 for differential expression? Some examples of PCA?
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Nov 20, 2022 The fact that from nothing i can do RNA sequencing from start to bottom Maybe tutorials with other tools from galaxy
Nov 7, 2022 Hands on data analysis, problem solving maybe notification of different tools with similar names? but really I guess it was fun problem solving
Nov 18, 2020 Everything worked and the steps didn't take too much time. ALso It was good to see the luminal data used. I don't think it was used in the prvious tutorials (although it may have been an option - I'll double check.) We did it any way. I'd like to see more discussion of what to make of these gene and process lists. The first go method came up with categories such as "cell" what to make of this? Also - the gene lists identified in these tutorials does not match that of the Fu paper. Probably because a smaller data set was used ?
Oct 3, 2019 very clear, good sample data
Aug 19, 2019 easy to follow. thank you for including a picture of the results for comparison more analysis/interpretation
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Feb 19, 2021 I like that it has a clear relation to the NGS topic, this helped to keep me motivated Actually it was very well developed, maybe one for heatmaps would be a great addition
Feb 17, 2021 well explained I would include some links with more options such as color palettes... shapes...
Feb 17, 2021 very concise and helpful !
Feb 15, 2021 very interesting library to visualize data
Oct 9, 2019 Would like to have more emphasis on actual data analysis and visualization. Too much time was spent on data frame functions. Morning session already provided good introduction to data handling basics.
Oct 9, 2019 Lot of different ways to manipulate data could be more taken into apart, several focuses, more focus to the vizualisation
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Jul 27, 2021 There is no code. For instance, how do you search your clusters for the marker genes?
Apr 3, 2021 clearly described, can be followed step by step, super tutorial for new users.
Mar 31, 2021 clearly described, can be followed step by step, idea for new-users.
Mar 12, 2021 I wanted to follow "Hands-on: Remove genes found in less than 3 cells" with tool "filter with scanpy", had given the every parameter correctly, but could not be successful every time.
Feb 18, 2021 Easy to follow tutorial. I learnt about so many tools used for data analysis.
Jul 22, 2020 Theres a copy-paste error in Cell type annotations in the first hands-on in the solution to the question. The "Annotated data matrix" should be another file.
Jul 19, 2020 The workflow for download has 4 imports (barcodes.tsv, genes.tsv, matrix.mtx and Pasted Entry) but ONLY Pasted Entry connects to the remainder of the workflow. This doesn't seem to match up to Import Data and the remainder of the workflow. Or, there is no obvious place when one would execute the workflow.
Jul 17, 2020 Independent self-paced learning. Assistance through the gitter chat (Galaxy Training Network/galaxy-single-cell) was appreciated twice. Two steps that I could not make work because of an incompatible newer version of a "plot with scanpy tool" and one step with a collection output (from Method used for plotting”: Marker genes: Plot ranking of genes as violin plot, using 'pl.rank_genes_groups_violin') that was unclear .
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Jun 9, 2020 I like that it exists It is either outdated for the current Galaxy modules or the Galaxy interface has had major changes. Many steps in this tutorial do not match up to Galaxy- I am unable to produce any results.
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Jul 21, 2020 Very useful and well detailed presentation
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Feb 18, 2022 very clear referencing of input files
Jan 25, 2022 This tutorial is impossible to do with the standard memory allotment of usegalaxy.org. RNA StarSolo requires too much memory to run for a data set of this size. I brought my file storage down to 8% of the standard allotment and it did not start for over a day. You should pick tools that people can use with the standard package or say so up front. It also makes it impossible to keep anything to re-run later.
Jul 27, 2021 Simple, straight-forward, focused benchmarking (or at least a comparison) to Cell Ranger
Feb 21, 2021 Tutorial video went too fast with no much explanation.
Feb 18, 2021 Very illustrative The link to the full pipeline 'A full pipeline which produces both an AnnData and tabular file for inspection is provided here.' directs to a file scrna_tenx.ga - what are .ga files and what program should be used for these?
Oct 29, 2020 Confirmed by @jennaj after a STARsolo fail by a new user: https://zenodo.org/record/3457880/files/Homo_sapiens.GRCh37.75.gtf does not autodetect OR redetect as a GTF datatype (GFF instead). Changing the datatype manually to GTF causes STARSolo to fail. This makes the very first step in the tutorial unusable (after getting data into the history/collection creation). ping @mtekman @hrhotz @blankenberg Happens at usegalaxy.org (v 20.09) and usegalaxy.eu (v 20.05). Format issue with the reference annotation?? If so, nothing obvious or I missed it but that must be what is going on
Sep 2, 2020 Clear instructions The Homo_sapiens.GRCh37.75.gtf file seems to not work
Jul 21, 2020 I cannot select a reference genome, and it when I try to load the Homo_sapiens.GRCh37.75.gtf file, it says that it is unavailable.
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Mar 27, 2022 The fact that there are pictures which helps more the understanding fro each step. Nothing
Mar 15, 2022 the brief exxplanation more explicit practical experience
Nov 8, 2021 the qs and answers and clear explanation of each step refer to which CLI tool commands can be used for each step
Jul 29, 2021 clear explanation of the barcodes/UMI and where/how to find that info in reads the 'plain' tabular file was a bit confusing and took a while to get in the right format
Feb 21, 2021 Handy Tutorial video went too fast with no much explanation.
Feb 17, 2021 what will the preprocessing be useful for - perhaps this should be explained?
Feb 17, 2021 I've never done a single cell analysis before! It was a little bit fast.
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Sep 24, 2022 Data made small enough to process it together in class Could you please correct the following typos: "Differentially expressed miRNAs" into "Differentially expressed mRNAs" in the section "mRNA data analysis > Filter.. Thanks!
Apr 23, 2021 I like all the indications step by step. Very clear. I would like to have some information about others parameters that are setted by default. I only correct one part where there are 2 mistakes. In "Filter significantly differentially expressed mRNAs" section, Hands-on: Extract significantly DE genes in point 3) Filter “Filter”: Differentially expressed miRNAs (replace by mRNAs) And in point 5) Filter “Filter”: Differentially expressed miRNAs (replace by mRNAs). This is about the text.
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Sep 25, 2022 very comprehensive, needed for the data that doesn’t have annotation file (GTF) please make a video with it. and a real data using in this tutorial from ncbi or else.
Jul 16, 2021 Had a bit of information on how to use trinity needs way more content, i dont know what i am doing or why when performing the steps. very unfinished tutorial and i felt like i learned nothing because it was so empty and confusing
Jun 11, 2021 Easy to follow for the most part. You forgot to describe how to create an hmm database for the hmmscan step. I think hmmbuild can be used for this, but more detail would be needed about what input to feed hmmbuild so it can generate a model that can be effectively used with hmmscan.
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Feb 16, 2022 literally where is the volcano plot code? you give every code except for the actual plot! so unhelpful
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Mar 29, 2022 Everything because all were new for me To be given the ability to conduct all parts of the tutorial, because some tools (in my condition) were not worked and I had to create a new account on another server in order to fulfill the tutorial.
Jan 24, 2022 The examples are still very buggy. Many of them do not work with the instructions as supplied. For example, the SalmonKallistoMtxTo10x instructions fails, most likely because the program is looking for a gz file when the tutorial example makes an unzipped file. The Droplet barcode rank plot exercise also crashes.
Nov 30, 2021 The instructions are clear, I really enjoyed it thank you! Notes for the versions of the tools so you can select them and go a little bit faster with the course.
Jul 2, 2021 Speak a bit slower and explain each file before moving on. Relate the theoretical apresentation with this part.
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Sep 15, 2022 Clear, straight forward, but also information rich.
Mar 31, 2022 Everything because all was new for me The tutorial video would be more detailed in some parts.
Jul 5, 2021 From find markers on I couldn't produce the desired output. If a folow the link in galaxy to Scanpy findMarkers it produces an empty table; if a seach this tool in galaxy, it produces complete tables but in the end I can't produce the plots with scanpy plot embebed (gives error). The video is to quick and does not explain what is being doing, it is just a lot of clicks. Taking in consideration the international audience, jargon should not be used. This is a shame, because it is such an interesting topic.
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Mar 31, 2022 the creation of plots and after the process of visualization and the try of understanding what I saw i think nothing
Mar 12, 2022 The tutorial was very informative and steps were defined clearly to perform the analysis... Overall, it was quite informative. However, it would be preferable to include a video tutorial for performing the analysis, where results can be thoroughly explained and the steps would be more easier to follow to perform the analysis for new users.

Using Galaxy and Managing your Data

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Mar 31, 2022 a little bit challenging to ordinary first time user do more videos
Mar 22, 2022 The fact that for the majority of the steps there are pictures that show you what you expect. All good
Mar 19, 2022 very useful and easy to understand workflows
Nov 12, 2021 Some steps and pictures need to be updated for the current version of usegalaxy.
Feb 15, 2021 How workflow idea was introduced.
Feb 15, 2021 Very helpful to rerun the same steps in one go instead of running each step individually! Workflows save time!!
Nov 29, 2019 Very detailed and most steps are well explained. I do not understand why under "Test the workflow", point 5 it says "Repeat until all input datasets are set.". The only input dataset is that of the genes of chromosome 22 as far as I understood. Second, the list of genes on chr22 have in the first place been extracted from UCSC. But this step is not included in the workflow, right? So, the workflow only starts with a dataset that needs to be copied to a new history if the workflow is to be applied to another dataset (i.e. genes of chr10)? Third, when running the workflow there is that option with multiple datasets. It would have been nice to mention and explain that.
Jan 16, 2019 Galaxy does not run the last step of the workflow (concatenate forward and reverse overlaps) - does not even appear in the history at all
Nov 15, 2018 Thorough step by step directions. Does not assume you know stuff already. Naming the output files was a little confusing, especially when I was left on my own to continue to name all the rest of them. Why doesn't the new name show up in the workflow boxes after you name them?
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Mar 17, 2022 Dataset manipulation
Mar 14, 2022 Clear explanation, useful content, thanks clear and useful enough
Mar 14, 2022 There is a typo as :"M117-ch_1 - family 117, mother, reverse (R) reads from cheek" under the section "About these datasets". It should have been "M117-ch_2"
Dec 2, 2021 La secuencia, además es sencillo y permite experimentar los ejercicios o comprobar y aprender la información teórica. Quizás algunas indicaciones son susceptibles de mejorar, en virtud de mejorar el desarrollo del ejercicio directamente en los escritos; en los tutoriales quizás la unificacion de ellos, hay autores que son muy especificos y llevan de la mano al estudiante.
Aug 11, 2021 The activity was interactive but some steps were not explit enough for a beginner The steps should be made more explicit for beginners to easily grasp
Apr 11, 2021 Very detailed walk-through the tutorial!
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May 24, 2021 Very informative and clear Nothing
Jul 1, 2019 Too long and too much details with screenshots to be able to gasp the main thing just with quick browse through material. Short summary of key points would be very helpful.
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Jul 8, 2022 Clear example of a great use case What to do if pulling from an FTP server that requires credentials
Mar 15, 2022 The options are pretty intuitive.
Mar 14, 2022 Good information on how to use the rule based uploader -
Mar 14, 2022 very useful for paired-end datasets for sequencing analysis nothing
Mar 14, 2022 Clear explanation and utility of the tool/process Excellent
Jul 1, 2021 The explanation was clear and I was able to follow the training without any problems. the quality of the image was not so good
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Oct 27, 2020 The introduction Well.. it was JUST an introduction. No details on the galaxy-R communication :)
Sep 27, 2020 Getting data in and out from Galaxy it is incomplete
Oct 9, 2019 good introduction starting process of the R studio from Galaxy should be more explained
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Jul 5, 2022 It is a useful feature. The syntax of the "Replace text" tool is not explained. Thus, it is only useful with the data collection of the tutorial, but it does not teach how to aply it to other collections with different element identifiers. It would be great if it explained why the "Find pattern" and "Replace with" boxes are filled that way.
Sep 29, 2021 The short list of ways to add group tags. How to add different group tags via workflow to members of a collection.
Feb 10, 2021 i like it!
Apr 21, 2020 The tutorial is helpful, but more info about the different tools and adjustments made to the starting files would be helpful. Similarity info on when it is better to tag file during an analysis would also be beneficial.
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Aug 27, 2021 It is clear and answered my questions I am new to Galaxy so it work worked for my needs as is...
May 24, 2021 Very clear Nothing
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Sep 12, 2022 Didn't know this feature! tag=paired is incorrect - should be tag:paired ???
Sep 12, 2022 Simple and clear
Apr 26, 2021 Clear and well explained Another example to work through.
Jan 26, 2021 Holy crap this is a cool feature! I still dream of the ability to set a title of a the output dataset before clicking EXECUTE
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Mar 25, 2022 practicality
Jun 11, 2021 very simple
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Nov 4, 2022 The instructions may not be up to date. I tried following them but what was described did not appear when I tried to follow. For example, there is no jupyter icon that comes up under visualizations.
Dec 15, 2021 was well explained. The tutorial looks nothing like what is one my galaxy web instance. Jupiter notebooks are not listed under visualizations but rather are under tools. The dialog that comes up when I launch Jupyter also does not look like what is in this tutorial. I can't figure it out based on what you have shown.
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May 28, 2022 hashtags!
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Apr 7, 2022 The tutorial was instructive and easy to follow. As a WSL user, I really loved this session. I got to learn about Planemo.

Variant Analysis

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May 30, 2022 Good balance between some slightly more 'in depth topics' and simple and to the point hand-on instructions. The 'Available on these Galaxies' information should be updates. For exmple, the tutorial can not be completed as it is in the Australian server (for example, there are not locally installed snpEff databases, so a previous step with snpEff Download is needed and then use the option 'Downloaded snpEff database in your history'. Can be done but is confusing specially for novices). On the other hand, as far as I know, it can be conducted exactly as it is in the European server, but that one is not listed in the 'Available on these Galaxies' drop down menu.
Sep 10, 2021 All of it My understanding now is that GEMINI is human only, so I followed this intending to do other species, but have to now find an alternative. Perhaps the title should be "Variant calling in humans" rather than "diploid systems"? Certainly would be useful to clarify the specificity of GEMINI in that step. But, thanks so much for doing this brilliant tutorial!
Jul 7, 2021 The data processing pipeline The tutorial should have each module version to avoid errors, GEMINIS is only available in the european server and the final exercises should contain the results from each GEMINIS query (atleast a number)
Nov 4, 2018 I'm still in the middle of it. But when doing snpEFF there is no refernece genome available. This tutorial does not say to download one. Other variant analyses say to download hg19. this is not available in the shared data folders. When using an hg19 fasta from another source freeBayes fails because it isn't indexed. Not sure how to index it. SnpEFF calls for a database. I downloaded one and am trying it now. But it would be good to include this step in the tutorial
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Nov 16, 2022 detailed explanation of variant calling and genotype calling
Nov 2, 2022 This tutorial gives a comprehensive overview about all analysis steps and important parameters involved. Where is the actual hands-on command code, which is generated after all parameter boxes have been checked, and the 'submit button' is clicked? Where are the actual tool commands for each step, a user would need to perform these analysis steps on the command line? I know these can be displayed in Galaxy, but it would be helpful to show them in the tutorials as well.
Mar 18, 2022 The step-by-step approach and the additional explanations for some input fields Perhaps an additional indication of which patch of the hg19 is recognised as the database of the SNPeff eff output of GEMINI load. It took me several attempts to realise that it must be the unpatched version.
Nov 17, 2021 Nice features and understandable handling for beginners Some data and tools are not at the described places; specifically genome annotation fasta and snpTools... snpEff is not existing, so I used snpEff eff; snpSift Annotate exists twice with different features. Description on how to create the pedigree file.
Jun 30, 2021 Oustanding material! Nothing!
May 26, 2021 all of it nothing - it's perfect
May 25, 2021 Gareth, Melissa and Khalid (I was in breakout room 3) were all incredibly helpful and it went at a good pace. It was VERY helpful getting the course material ahead of the workshop, which allowed time to familiarise myself with the content. I think it was on the mark for me.
Mar 30, 2021 Going to use this in Australia soon (late May 2021)- excited about it. More feedback to come afterwards no doubt! I can see in the intro that this tutorial is set up for raw (fastq) and BAM data entry points. This is great but I was hoping you could include a workflow for fastq to BAM. I realise it is in the full workflow so I took the liberty of comparing the two offered workflows and trimmed down to a QC to BAM workflow (https://usegalaxy.org.au/u/gareth-qfab/w/copy-of-exome-seq-training-full-w-cached-ref-imported-from-uploaded-file ). I understand we can do this elsewhere but good to have it consistent within this tutorial. Tested on Zenodo data and works fine. Thanks, Gareth
Feb 19, 2021 Concentration on the essential aspects with the possibility to further deepen the knowledge about the individual tools
Jun 12, 2020 I liked that it was very specific and went step by step on how to do everything. nothing was left out. I would like to know how to take the vcf file and identify polymorphic sites in all three individuals.
Mar 25, 2020 Clear, stepwise Gemini load dialog in usegalaxy.eu suggested the SnpEff eff output file was 'unavailable' to use. It made me go back and check things before pressing on regardless. Not a problem with the tutorial per se. Thanks
Mar 12, 2020 Very accessible, especially if you compare the galaxy ui to something like bash. -
Jul 26, 2019 Even simple steps were explained.
Jul 26, 2019 looking at genes
Dec 26, 2018 unfortunately in compare with others tutorial, this is very unclear and o'm not satisfied please improve this very important tutorial with clear and accurate dive.
Nov 4, 2018 I like the idea of it It seems impossible to complete. The training data is not available in the shared data link. If it is, it's too hard to find. A more general point would be to explain how the tutorial could be used on other data sets. or ref genomes. For this I tried using an hg19 fasta file from another data set, but got an error about indexing. So I guess, explaining how the training data sets are pre-formatted would help when trying to use sets from other sources
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Nov 4, 2018 I like the idea After running the FreeBayes I ended up with 2 variants instead of 30. And so got stuck there. Also it's not clear why the filtering and subsequent steps would be done on the markduplicates output, rather than the left align output. Why do the leftalign if we don't use that output again? I did both and got the same results. Overall I am finding the galaxy experience to be rather frustrating. I'm trying to decide whether to incorporate these tutorials in my class, but often I can't find the necessary input data, get unexplained errors, or get output different from the tutorial
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Jul 20, 2021 The step by step procedure If you have time, please add further analysis of the SNP (when we search snippy in galaxy, it shows two snippy programs, only of the them is showing right result) please try to correct it (if m not mistaken)
Apr 7, 2021 This tutorial works with the input files. However, working with non-model organisms is a problem. Download the genbank entry is nice, but which one - on BioSample or else? What should it look like? Any requirements? Only the easy way is shown. How can a reference genome fasta be used along with a gff3 file? That does not work at all with files other than built in or sample files. The tutorial is meant well, but it should be improved to enable also people not working with yeast, mouse or human to use it and prevent problems. Thanks a lot!
Jul 24, 2019 The step "Select all outputs" in "Hands-on: Run Snippy" is not obvious what to do exactly.
Nov 4, 2018 This was very straight forward and ran well (once it was clear that it only runs on the eu site). listing the file types was useful maybe link to descriptions of the various file type generated/used
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Sep 14, 2022 its step by step steps are not explained - for example: why do i need align left, why do i need to refilter quality levels...? Way to hard to understand. More Explanation why things are done a certain way. Its not explained why certain values are set and how to choose the right values. This tutorial is way to complicated.
Mar 18, 2022 The additional explanations of the individual configuration options within the tools, especially the SQLite Syntax.
Nov 19, 2021 It is structured well and well explained. It might be helpful to mention the alternative tools and solutions
Jul 6, 2021 The detailed steps were very useful to get started and this would help me do advance analysis as well.
Feb 25, 2021 the work flow and associated explanations. Perfect for my students to get acquainted with the workflow, inputs and outputs, and then move to HPC learning incorporate UMI-based workflows (e.g., duplex consensus)
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Feb 5, 2021 Achievable within 2hrs Some clarity on assumptions such as recessive mutation and the purpose of the mapping strain (for non-geneticists). And SnpEff4.1 is no longer available. Can this be patched?
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Jul 2, 2022 The clear instructions on how to use the tools allowing learners to supply the solution and evaluating the answers
Mar 26, 2022 Tutorials easy to follow This is great model of learning
Mar 23, 2022 I like that even though we do not have to type in commands, we still have steps to follow. I have made errors but still were able to use tools to rectify. One can play around till the correct output! Specification of version to use as we ended up getting different answers due to using default version
Mar 23, 2022 the hands on helped with grasping tasks Requires much more time
Mar 22, 2022 I like the step by step instructions on what to do It would be better if the tutorials should also be in video form for easy understanding
Mar 22, 2022 overall the tutorial was easy to go through sometimes it was unclear where some of the errors came from and how they can be fixed
Mar 22, 2022 Sequence analysis
Jul 2, 2021 The step-by-step description help a lot!. Thank you
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Sep 1, 2021 how to work on my on data
Aug 10, 2021 terrible instructions
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Aug 12, 2021 The tutorial is very detailed
Aug 12, 2021 Great flow of tutorial Not much
Aug 11, 2021 I liked how detailed every steps were taught !
Aug 11, 2021 The way one can understand the relation between different organism through the clades.
Aug 11, 2021 Great interactive learning combining both theory and practice
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Visualisation

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Jan 4, 2022 The simplicity The tool is pretty solid
Aug 19, 2021 nothing, I loved it very clear and well explained!
Jul 2, 2021 Provide a simple example of visualizing a genome with annotation
Feb 18, 2021 that there were several examples
Feb 25, 2020 Everything Further tutorials like this one