Renaming duplicate transcripts for Ensembl

thelovelab / tximeta

Transcript quantification import with automatic metadata detection

https://thelovelab.github.io/tximeta/

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Renaming duplicate transcripts for Ensembl #7

Closed mikelove closed 5 years ago

mikelove commented 5 years ago

Don't use the haplotype chromosome transcript ID, but figure out the one on the "standard chromosome"

stephenturner commented 5 years ago

see also COMBINE-lab/salmon#249 @afkoeppel

mikelove commented 5 years ago

I’ve hopefully fixed this with e29c460

mikelove commented 5 years ago

Details: cleanDuplicateTxps=TRUE will swap out haplotype chromosome transcripts for standard chromsome transcripts that are exact sequence duplicates. Needs some testing which I will do this week but let me know if it works for you.