Identify ORFs with gffread

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5.7 years ago

harry.smith • 0

Hello,

I have read a few papers that say they identify ORFs using gffread (cufflinks), but are not very detailed in how they do this. I have gtfs generated from gffcompare (stringtie) and have looked over the -h options from gffread, but am not sure exactly how to proceed. I think it makes sense to use gffread since the files I have now come from the same workflow, but could use some help using the right syntax.

Thank you Harry

RNA-Seq genome sequence • 1.9k views

ADD COMMENT • link 5.7 years ago by harry.smith • 0

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How To Extract Cds And Protein Sequences From Cufflinks Transcripts.Gtf File?

In case you are not automatically redirected, the link to the TransDecoder wiki is https://github.com/TransDecoder/TransDecoder/wiki, and the section has the same title: Starting from a genome-based transcript structure GTF file (eg. cufflinks or stringtie).

ADD REPLY • link 5.7 years ago by h.mon 35k

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Thank you. This looks like exactly what I need.

ADD REPLY • link 5.7 years ago by harry.smith • 0

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