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mortazavilab / TALON

Technology agnostic long read analysis pipeline for transcriptomes
MIT License
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Talon GTF - adding CDS #71

Closed rsalz closed 3 years ago

rsalz commented 3 years ago

Hi,

I was wondering if there was a simple way to add features to the talon GTF such as CDS. Any recommendations?

TIA Renee

fairliereese commented 3 years ago

For known transcripts, you could do this with a reference annotation that already has the CDS annotated (outside of TALON) and somehow merge it with the TALON GTF output. However since TALON is specifically designed with novel transcripts in mind, it would be difficult to get the CDSs of these specific transcripts which don't have annotated CDSs.

I would advise trying to look for CDSs as a post-TALON analysis. For novel transcripts you could use something like TransDecoder which predicts ORFs and the most likely CDS from each transcript model. This has worked for our post-TALON analysis in the past. However, adding such functionality to TALON itself I believe is beyond the scope of the software.