Frequently Asked Questions
Igv
Add Mapped reads track to IGV from Galaxy
- Install IGV (if not already installed)
- Launch IGV on your computer
- Check if the reference genome is available on the IGV instance
- Expand the BAM dataset with the mapped reads in the history
- Click on the
local
indisplay with IGV
to load the reads into the IGV browserSwitch to the IGV instance
The mapped reads track should appear. Be sure that all files have the same genome ID
Add genome and annotations to IGV from Galaxy
- Upload a FASTA file with the reference genome and a GFF3 file with its annotation in the history (if not already there)
- Install IGV (if not already installed)
- Launch IGV on your computer
- Expand the FASTA dataset with the genome in the history
- Click on the
local
indisplay with IGV
to load the genome into the IGV browser- Wait until all Dataset status are
ok
Close the window
An alert
ERROR Parameter "file" is required
may appear. Ignore it.- Expand the GFF3 dataset with the annotations of the genome in the history
- Click on the
local
indisplay with IGV
to load the annotation into the IGV browserSwitch to the IGV instance
The annotation track should appear. Be careful that all files have the same genome ID
Visualisation
Using IGV with Galaxy
You can send data from your Galaxy history to IGV for viewing as follows:
- Install IGV on your computer (IGV download page)
- Start IGV
- In recent versions of IGV, you will have to enable the port:
- In IGV, go to
View > Preferences > Advanced
- Check the box
Enable Port
- In Galaxy, expand the dataset you would like to view in IGV
- Make sure you have set a reference genome/database correctly (dbkey) (instructions)
- Under
display in IGV
, click onlocal
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