Introduction to DNA Methylation data analysis

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# Introduction to DNA Methylation data analysis

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		Authors: 
<a href="/training-material/hall-of-fame/joachimwolff/" class="contributor-badge contributor-joachimwolff"><img src="https://avatars.githubusercontent.com/joachimwolff?s=27" alt="Avatar">Joachim Wolff</a>

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<div class="footnote" style="bottom: 8em;"><i class="far fa-calendar" aria-hidden="true"></i><span class="visually-hidden">last_modification</span> Updated: Jul 26, 2021</div>

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## Requirements

Before diving into this slide deck, we recommend you to have a look at:

- [Introduction to Galaxy Analyses](/training-material/topics/introduction)

- [Sequence analysis](/training-material/topics/sequence-analysis)
    - Quality Control: [<i class="fab fa-slideshare" aria-hidden="true"></i><span class="visually-hidden">slides</span> slides](/training-material/topics/sequence-analysis/tutorials/quality-control/slides.html) - [<i class="fas fa-laptop" aria-hidden="true"></i><span class="visually-hidden">tutorial</span> hands-on](/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html)
    - Mapping: [<i class="fab fa-slideshare" aria-hidden="true"></i><span class="visually-hidden">slides</span> slides](/training-material/topics/sequence-analysis/tutorials/mapping/slides.html) - [<i class="fas fa-laptop" aria-hidden="true"></i><span class="visually-hidden">tutorial</span> hands-on](/training-material/topics/sequence-analysis/tutorials/mapping/tutorial.html)

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## DNA Methylation data analysis
## --
##Bisulfite sequencing QC and processing in Galaxy

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#Biological background

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![Cartoon of a mitotic chromosome zoomed in to show dna and histones and nucleosomes, further zoomed in to show individual DNA strands with methylated dna.](../images/genome_organization.jpeg)

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.image-75[![A picture from a paper with at top a cartoon of a chromosome and the chromatin, pointing to a single nucleosome, and the histone and dna methylation modifications possible. Below is a comparison of a switched on gene with active or open chromatin and unmethylated cytosines, and acetylated histones. Below is a switched off gene with condensed chromatin, methylated cytosines, and deacetylated histones.](../images/modification_methylation.jpeg)]

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#Methylation: What is it good for?
- Suppression of repeats
- Gene expression
- Imprinting
- X-chromosome inactivation
- Chromosome stability
- Development
- Changes in cancer
- Changes with age

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#Heritable methylation

.image-50[![Another paper chart, here a number of graphs are shown, but their interpretation is unclear.](../images/heritable_methylation.png)]
.image-25[![Another set of graphs from the same paper and a picture of a mouse and its baby suggesting heritability.](../images/mouse.jpg)]

<small>Weaver et al. Nature Neurosci 2004; 7: 847-854</small>

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#More than 5-mC
.image-75[![A schematic of a chemical pathway affecting cytosine and various transformation that can occur. Some have arrows indicating gene silencing or activation.](../images/more_than_5-mC.png)]

<small>Mariani et al. (2013) Cancers</small>

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# [Hands-on](/training-material/topics/epigenetics/tutorials/methylation-seq/tutorial.html)
##Step number 1: load data and run FastQC

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# Bisulfite sequencing
.image-75[![Cartoon of a methlated gene sequence and bisulfite conversion  replacing a C with a U. Below that is sequenced and the resut is reconstructed to figure out which Cs were methylated (because they weren't replaced with Us.)](../images/bisulfite_sequencing.png)]

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# Mapping a bisulfite sequence read
.image-75[![Illegible graphic from a paper showing reconstruction of methylated sequences.](../images/Mapping_a_bisulfite_seq_read.jpeg)]

<small>Krueger et al.</small>

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# For the morbidly curious
####For SE datasets or read number 1 in PE:
- C→T converted read: OT or OB (original strand)
- G→A converted read: CTOT or CTOB (complementary strand)
- C→T converted genome: OT or CTOB (top physical strand)
- G→A converted genome: OB or CTOB (bottom physical strand)

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# [Hands-on](/training-material/topics/epigenetics/tutorials/methylation-seq/tutorial.html)
##Step number 2: Alignment and methylation bias

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#Methylation bias
.image-75[![line chart showing position along mapped read and CpG methylation percent. It is a wavy overlapping set of lines.](../images/methylation_bias.png)]

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#Methylation extraction

```txt
track type="bedGraph" description="SRR1182519.sorted CpG Methylation levels"
1	25114	25115	100	2	1
1	25115	25116	100	3	1

track type="bedGraph" description="SRR1182519.sorted merged CpG Methylation levels"
1	25114	25116	100	5	1
```

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# [Hands-on](/training-material/topics/epigenetics/tutorials/methylation-seq/tutorial.html)
##Step number 3: Visualization and more

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#Thanks for your attention!

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## Related tutorials

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## Thank You!

This material is the result of a collaborative work. Thanks to the [Galaxy Training Network](https://training.galaxyproject.org) and all the contributors!

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<a rel="license" href="https://creativecommons.org/licenses/by/4.0/">
This material is licensed under the Creative Commons Attribution 4.0 International License</a>.