transMap tracks on new assemblies have wrong amino acid labels on negative strand

ucsc-mus-strain-cactus / build_browser

Build a UCSC brower from a progressiveCactus alignment

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transMap tracks on new assemblies have wrong amino acid labels on negative strand #13

Closed ifiddes closed 9 years ago

ifiddes commented 9 years ago

See http://hgwdev-mus-strain.cse.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=ifiddes&hgS_otherUserSessionName=transmap_error

That is an inframe stop for ENSMUST00000128731.3, TGG -> TGA. The track shows a Tryptophan (W), which is the original TGG, but it is highlighted in red, so something knows that there is a problem there.

joelarmstrong commented 9 years ago

I think the track is meant to show the differences in J relative to NJ, much like the snakes, so this is probably intended. Maybe the other way around would make more sense for this use case though.

diekhans commented 9 years ago

this is control by the rendering mode. It's show mRNA codons, which for transmap, these are the codons in the other species. You can change this if you like in the track controls.