Closed xiekunwhy closed 1 year ago
Hi,
I found that just a few transcripts with final stop_codon in gtf when giving --gtf option.
grep -w transcript par.mp.raw.gtf|wc -l 127776 ## keep transcript with final stop_codon but without in-frame stop_codon gffread -g par.fa -J -T par.mp.raw.gtf -o par.mp.raw.J.gtf grep -w transcript par.mp.raw.J.gtf|wc -l 146 ## keep transcript without in-frame stop_codon gffread -g par.fa -V -T par.mp.raw.gtf -o par.mp.raw.V.gtf grep -w transcript par.mp.raw.V.gtf|wc -l 104905
as we can see, many transcript do not include final stop_codon.
Best, Kun
I solved this problem by writing a script to covert gff to gtf.
Hi,
I found that just a few transcripts with final stop_codon in gtf when giving --gtf option.
as we can see, many transcript do not include final stop_codon.
Best, Kun