ENSEMBL chromosome names (e.g., 1 instead of chr1) don't work in desktop app

[Gennady Margolin]

Hi,

I have IGV 2.17.4 on mac (it was the same with 2.17.1). 

I load zebrafish genome danRer11/GRCz11 which has chr1, chr2 etc. My bam file alignments are to 1, 2 etc.

I think previously IGV had a mapping that allowed this to work, but not anymore, apparently.

The web app shows my bam files, but the desktop does not. I think this feature was working previously.

Looking at some old thread from 2017 https://github.com/igvteam/igv.js/issues/302 they say towards the bottom:

"The other built-in default is an alias table between "chr1" and "1" naming conventions. This is to allow annotation and track files to use both conventions."

I'd appreciate if anyone can offer a solution!

Thanks!

[Gennady Margolin]

I just installed desktop 2.16.2 version and there it works. It looks like from 2.17 something went wrong ...

[igv-help]

Hi, could you try updating your danRer11 genome file by selecting it from "Genomes > Select Hosted Genome...".   If that doesn't fix the issue let us know.

[Gennady Margolin]

Hi, that fixed it - thanks so much!