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igvteam / igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
https://igv.org
MIT License
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.bed and .bedpe tracks not loading in IGV 2.17.4 #1521

Closed virpa81 closed 5 months ago

virpa81 commented 6 months ago

Hello! I just uploaded IGV to 2.17.4 and suddenly all of my .bed or .bedpe tracks can no longer be visualised in my user session. I tried re-loading them in a new session, but without results. I do not get any error message as I load the tracks. The track "slot" does appear, but there is no content.

Screenshot

I am working on a Macbookpro with macOS Monterey 12.7.5.

The format of by bed files is as follow:

7 33732998 33733703 16 27306094 27307036 9 10747618 10749089 5 3169503 3170944

The format of the bedpe files as follow:

20 1195000 1200000 20 1235000 1240000 . . . . 34,139,34 Common 20 3335000 3340000 20 3420000 3425000 . . . . 34,139,34 Common 20 3830000 3840000 20 3900000 3910000 . . . . 150,255,0 B 20 3830000 3840000 20 3910000 3920000 . . . . 0,255,150 A

Does anyone have any idea how to solve this?

jrobinso commented 5 months ago

Try refreshing the Zebrafish menu assembly from the Genome menu (Select Hosted Genome...). Let us know if that fixes the problem.

This is probably a chromosome name problem (the names in the assembly are chr7, chr16, chr9, etc, not 7, 16, 9). There is a patch for this in the assembly json, but you might have an older one cached.

virpa81 commented 5 months ago

This solved the issue! Thank you very much!