Hi @bwlang !!
The genome might be in IGV already but maybe not installed into your local copy? By default not everything is pre-loaded. There is an import function in the menu functions where you can check. If not available, then yes, you’ll need to index the custom genome in both places if you want to load multiple files into the same view, and have the base-level details.
Then, if your datasets in Galaxy have the same database (dbkey), when you use the link out the transfer function will route without both indexing steps. That database can be native to the Galaxy server or a custom build you create in your Galaxy account. Same for IGV. The genomes need to be “exact” of course, e.g. same chromosome identifiers/lengths or an error can come up.
Adding a summary since it hasn’t been posted in a while.
How to link data between Galaxy and IGV
Single file display based on coordinates without base-level details
- Use the link to IGV under a dataset’s visualization display function
- 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
- Reference Genome is indexed in IGV (native or custom)
- Reference Genome is indexed in Galaxy (native or custom)
- Reference Genome is exactly the same assembly/build and given same database (dbkey) in both
- Dataset(s) assigned that database (dbkey)
- Use the link to IGV under a dataset’s visualization display function
Let me know if that is enough info or not! Jen