search

Gaius-Augustus / BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
Other
334 stars 80 forks source link

Convert gtf to gff3 #801

Closed tanpham15 closed 2 months ago

tanpham15 commented 2 months ago

Hi,

I didn't specific an option -gff3, but I got the result as braker.gtf.

Now I want to convert gtf to gff3, can I use "gffread"?

Because after running gffread -E braker.gtf -o braker.gff3, it provides result but also has warning:

Warning: discarding unrecognized feature (no ID or Parent):
scaf1   GeneMark.hmm3   gene    15810   21127   .       -       .       g2
Warning: invalid GTF record, transcript_id not found:
scaf1   GeneMark.hmm3   transcript      15810   21127   .       -       .       g2.t1
Warning: discarding unrecognized feature (no ID or Parent):
scaf1   GeneMark.hmm3   gene    27124   32408   .       -       .       g3
Warning: invalid GTF record, transcript_id not found:
scaf1   GeneMark.hmm3   transcript      27124   32408   .       -       .       g3.t1

Is that good to use this gff3 file? If not, which program should I use for converting

Thank you very much for your time Tan

tanpham15 commented 2 months ago

I found the solution in #640