search

MonashBioinformaticsPlatform / RNAsik-pipe

RNAsik - more than just a pipeline
https://monashbioinformaticsplatform.github.io/RNAsik-pipe/
Apache License 2.0
13 stars 5 forks source link

Use any of gene, exon, transcript, CDS in get_geneids.py #38

Closed pansapiens closed 5 years ago

pansapiens commented 5 years ago

This appears to work for iGenomes annotations, addressing https://github.com/MonashBioinformaticsPlatform/RNAsik-pipe/issues/30.

pansapiens commented 5 years ago

For Homo_sapiens/UCSC/hg38, this actually still fails to generate output in the *-withNames-proteinCoding.txt file, probably because the Homo_sapiens/UCSC/hg38 GTF doesn't contain biotype fields and mk_cnts_file.py only works for protein_coding (not NA biotypes, as they will be in this case).