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thelovelab / tximport

Transcript quantification import for modular pipelines
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ignoreAfterBar does not apply with txOut=T and countsFromAbundance != "no" #38

Closed karl616 closed 4 years ago

karl616 commented 4 years ago

Thank you for an eminent and very convenient software.

I'm importing kallisto data from h5 files and want output the transcripts. With Gencode as a reference this comes with an inconvenient transcript naming adding |-separated information after the transcript ID. Exporting genes, this is handled by the ignoreAfterBar flag, but this never takes effect when exporting transcripts:

https://github.com/mikelove/tximport/blob/master/R/tximport.R#L578-L595

Is this intentional?

mikelove commented 4 years ago

Yes, essentially you can modify transcript names with a one liner as you like. The reason that the argument exists is because the transcript-to-gene matching occurs inside the function.