Add genome and annotations to IGV from Galaxy

1. Upload a FASTA file with the reference genome and a GFF3 file with its annotation in the history (if not already there)
2. Install IGV (if not already installed)
3. Launch IGV on your computer
4. Expand the FASTA dataset with the genome in the history
5. Click on the local in display with IGV to load the genome into the IGV browser
6. Wait until all Dataset status are ok

7. Close the window

   An alert ERROR Parameter "file" is required may appear. Ignore it.

8. Expand the GFF3 dataset with the annotations of the genome in the history
9. Click on the local in display with IGV to load the annotation into the IGV browser

10. Switch to the IGV instance

    The annotation track should appear. Be careful that all files have the same genome ID

Still have questions?

Want to embed this snippet (FAQ) in your GTN Tutorial?

{% snippet  topics/assembly/faqs/visualizations_igv_add_genome.md %}