X Chromosome Genes

[Caseng Zhang]

Hi there!

Recent user of LocusZoom. Thank you for all of you work maintaining it and creating it. We are doing an X Chromosome analysis. The Manhattan Plot generates with no issues, but it appears as though there is no gene information (all SNPs say no nearby genes). Does LocusZoom not typically populate genes for the X chromosome or is there are error on my end?

Thanks!

 

[Andy Boughton]

One possibility would be to check that the correct genome build is specified, as otherwise your coordinates might be pointing to a region that (in that build) didn't have any interesting genes.

The library used to locate genes is here if you want to probe more deeply:

https://pypi.org/project/GeneLocator/

Unfortunately, I no longer work at UM, and cannot offer support or updates for datasets in Locuszoom.org (perhaps someone else on this list could). Hopefully this gives you a place to get started debugging, though!

-Andy Boughton

abo...@umich.edu

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