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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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bisulfite mode in small letter reference sequences "disabled" #335

Closed aerval closed 7 years ago

aerval commented 7 years ago

I am displaying WGBS data on the default mm10 genome that contains at some positions in the reference genome small letter bases (repeats etc.?) like act instead of ACT. The default bisulfite mode does not highlight the methylation in reads in these areas. Similar, C highlighting does not highlight Cs etc. I assume its a bug because CpGs are recognized by capital CG letters?

Edit: Of course you can create an all capital version of the reference genome to fix the display

jrobinso commented 7 years ago

Hi, yes that looks like a bug. Could you please try the development snapshot version and see if that resolves the problem? You can access it here: http://software.broadinstitute.org/software/igv/download_snapshot

aerval commented 7 years ago

Brilliant, that works great. Thanks a lot!

aerval commented 7 years ago

Oh, well it is not important for me but the coverage plot still does not show the number of un-/methylated Cs. Really not important as you can easily look it up but yeah ...

jrobinso commented 7 years ago

OK, coverage plot should be fixed now (snapshot version). These fixes will be in the next release.