gffread: warnings when converting to GTF
Hello,
I have a GFF file that I am trying to convert to GTF with gffread using the following code:
gffread -E file.gff -T -o- > file.gtf
While I do get a gtf file as an output, there two error messages that come up many times:
"Warning: exon feature found before transcript ID (Transcript ID)"
"Warning: adjusted transcript (Transcript ID) boundaries according to terminal exons."
Has anyone gotten these warnings before, or know how to fix them? Thank you!
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arussell3483 •
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You can also try other solutions to perform your conversion. See a mini-review here.
To be sure that the
exon feature found before transcript IDis not lost you can check with anawkcommand or withagat_sq_stat_basic.plfrom AGAT if all the exons from the GFF file are still present in the GTF file.Thanks! I ended up using AGAT since some of the features weren't conserved with gffread, as well. AGAT worked great!