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[jennaj]

Hi @cjain

Great, glad that helped!

For visualization, use the link inside of a dataset like this:

You will need to have IGV set up on your own computer. We have tutorials here to get you started.

• GTN Materials Search (query=igv)

More help is at this forum in topics with the igv tag. This is a simple quote from one of them.

@jennaj

You reference genome fasta should be formatted in a very simple way. We have a guide here → FAQ: How to use Custom Reference Genomes?

Then, your GFF3 needs to be based on that exact same genome.

More instructions are in this topic

@jennaj

How to link data between Galaxy and IGV

Single file display based on coordinates without base-level details

1. Use the link to IGV under a dataset’s visualization display function
2. Wait for the one-off indexing to complete, and you’ll be automatically redirected

Single or Multiple file display based on coordinates with base-level details

1. Reference Genome is indexed in IGV (native or custom)
2. Reference Genome is indexed in Galaxy (native or custom)
3. Reference Genome is exactly the same assembly/build and given same database (dbkey) in both
4. Dataset(s) assigned that database (dbkey)
5. Use the link to IGV under a dataset’s visualization display function

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Hope this also helps!