Question: Identify ORFs with gffread
0
gravatar for harry.smith
9 months ago by
harry.smith0 wrote:

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 sequence genome • 293 views
ADD COMMENTlink written 9 months ago by harry.smith0
1

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 REPLYlink modified 9 months ago • written 9 months ago by h.mon25k

Thank you. This looks like exactly what I need.

ADD REPLYlink written 9 months ago by harry.smith0
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