Question: Identify ORFs with gffread
gravatar for harry.smith
21 months ago by
harry.smith0 wrote:


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 sequence genome • 617 views
ADD COMMENTlink written 21 months ago by harry.smith0

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, and the section has the same title: Starting from a genome-based transcript structure GTF file (eg. cufflinks or stringtie).

ADD REPLYlink modified 21 months ago • written 21 months ago by h.mon29k

Thank you. This looks like exactly what I need.

ADD REPLYlink written 21 months ago by harry.smith0
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