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thelovelab / tximeta

Transcript quantification import with automatic metadata detection
https://thelovelab.github.io/tximeta/
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Change genome build to GRCm39 for GENCODE release M26 and later #77

Closed csoneson closed 9 months ago

csoneson commented 9 months ago

Hi @mikelove - we just noticed that the recent GENCODE mouse releases are still linked to GRCm38: https://github.com/thelovelab/tximeta/blob/devel/inst/extdata/hashtable.csv#L24-L31

I believe that from version M26, this should be GRCm39 (https://www.gencodegenes.org/mouse/releases.html). We noticed since when importing data quantified against a new GENCODE version, tximeta would complain that some features were out of bounds.

This PR changes the genome build for GENCODE vM26 and later.

mikelove commented 9 months ago

Thanks for catching this! I'll push to release and devel.

mikelove commented 9 months ago

Thanks, I've pushed and added a note to news for release and devel.