dm6 gene names on chromosomes other than chrX are not found
Closed this issue · 4 comments
I run data on the Drosophila dm6 genome and noticed that only genes from chrX are recognized and found (search box or via showGenomicRegion), but no gene on other chromosomes
igv <- igvR()
setBrowserWindowTitle(igv, "igvR Dmel")
setGenome(igv, "dm6")
showGenomicRegion(igv, "w")
[1] "w"
showGenomicRegion(igv, "Msp300")
[1] "unrecognized locus 'Msp300'"
The transcript of Msp300 is present in the track view and I can navigate their with coordinates, just not by gene. The standalone igv program can find those genes.
@gvogler - working on this now, taking some notes.
Msp300's coordinates: chr2L:5,100,877-5,207,002
bypassing igvR/javascript message passing, trying your test case in the javascript browser console, I think the problem lies in igv.js. I will put the question to Jim Robinson, who is always responsive and helpful.
igv.version() // '2.10.5'
p1 = igvBrowser.search("chr2L:5,100,877-5,207,002") // this works
p2 = igvBrowser.search("Msp300") // this fails
search returns a Promise which, when examined for each of these cases, looks like this:
@gvogler Jim Robinson says this is now fixed: igvteam/igv.js#1476 (comment)
Could you give it a try?
Perfect! Works like a charm.
glad to hear it!