gffread: warnings when converting to GTF

Question

[arussell3483]

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!

[Juke34]

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 ID is not lost you can check with an awk command or with agat_sq_stat_basic.pl from AGAT if all the exons from the GFF file are still present in the GTF file.

[arussell3483]

Thanks! I ended up using AGAT since some of the features weren't conserved with gffread, as well. AGAT worked great!