IGV Web App: No Longer Recognizes Gene Names

[jvanbelzen]

I’ve used IGV Web App for a couple years to browse the sacCer3 genome. In the past, you could simply enter a Gene Name in the search box and the you would automatically be directed to the appropriate chromosome and location. For instance, in the past searching “PGK1” would automatically direct you to the the gene location. However, now an error is thrown: “Unrecognized locus: PGK1”. The same is true when searching with the Systematic Name “YCR012W”.

This feature stopped working several months ago (perhaps specific to sacCer3?) and I wanted to alert you of the problem. It makes browsing the genome much more challenging, as it appears that only coordinates are accepted, for instance: “chrIII:137,700-139,100”

Please consider re-implementing the ability to search by gene name.

[jrobinso]

Thanks for the report, this is fixed.

[KamrynG24]

Hello,

I am having the same issue on the sus scrofa 11.1 genome. It is not showing the annotation for PRKACA by name, gene ID, or location coordinates despite it being in the genome annotations, indicated in the link below.

https://www.ncbi.nlm.nih.gov/datasets/gene/GCF_000003025.6/?search=PRKACA

[jrobinso]

Not all genes will be recognized, only those in our default annotation set (https://hgdownload.soe.ucsc.edu/goldenPath/susScr11/database/refGene.txt.gz in this case).

Try loading this assembly from Genark (under the Genomes > UCSC Genark menu).