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igvteam / igv-webapp

IGV Web App
https://igv.org/app
MIT License
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How to load NCBI Mmul_10 genome using URL in IGV Web Browser? #278

Closed pbuendia closed 2 months ago

pbuendia commented 9 months ago

How do I load NCBI Mmul_10 genome using URL in the IGV Web Browser? I am trying to avoid downloading and uploading to IGV Web Browser but also wondering what the URL option is for or where it should link to?

This is the NCBI Mmul_10 genome URL: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_003339765.1/

Thanks you for your help!

Paty

jrobinso commented 9 months ago

In the current release at igv.org/app the URL needs to be to an igv.js genome json file, describe [here] (https://github.com/igvteam/igv.js/wiki). However we are just finishing testing on the next release which will allow loading of any assembly from the UCSC genark site. The URL for Mmul_10 is

CORRECTION https://hgdownload.soe.ucsc.edu/hubs/GCF/003/339/765/GCF_003339765.1/hub.txt

You can try this from https://igv.org/app-test. There are 2 options for loading the assembly. Loading from the Genomes | URL option will result in a sequence and annotation track, with other track options available from the "Tracks" menu. Loading from the Session | URL menu will result in a larger set of initial tracks. In both cases remaining tracks are available from the "Tracks" menu. Prior to release these options will probably be consolidated under the "Genomes" menu.

jrobinso commented 2 months ago

This has been released, so follow instructions above at https://igv.org/app