Add genome and annotations to IGV from Galaxy
Authors:
Delphine Lariviere
Bérénice Batut
Helena Rasche
Saskia Hiltemann
hall-of-fameAdd Contributions!
- 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 browser -
Switch to the IGV instance
The annotation track should appear. Be careful that all files have the same genome ID
Still have questions?
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Want to embed this snippet (FAQ) in your GTN Tutorial?
{% snippet topics/visualisation/faqs/visualizations_igv_add_genome.md %}