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openvax / topiary

Predict mutated T-cell epitopes from sequencing data
Apache License 2.0
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NCBIM37 #47

Closed gmicevic closed 8 years ago

gmicevic commented 8 years ago

What is the --reference-name for mm9 (NCBIM37) ? Thank you.

iskandr commented 8 years ago

Hey @gmicevic,

It looks like we only added GRCm38 to pyensembl (https://github.com/hammerlab/pyensembl/blob/master/pyensembl/species.py#L176), I'll try to fix that tomorrow.

Sorry, Alex

gmicevic commented 8 years ago

Great, that would help a lot. Thank you.

iskandr commented 8 years ago

Hey @gmicevic,

It turns out that this hits an open problem in how we've been treating references: though the UCSC and Ensembl's references are similar they are not, unfortunately, identical. We've been chugging along by treating, for example, hg19 as GRCh37. I'm going to write a quick/dirty fix right now which treats mm9 as GRCm37 but there will be differences in terms of names for unplaced or alternate contigs.

iskandr commented 8 years ago

@gmicevic Do you mind updating your versions of varcode, gtfparse, & pyensembl and trying again? You'll have to first run pyensembl install --release 67 --species mouse.