As an example, I'm working with a reference genome for pineapple and need a GTF and GFF file. This is the assembly ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/162/155/GCA_902162155.2_F153.v0709/
All that's available is a .gbff file. I'm looking for a way to convert this into a gff3 and gtf file.
I am able to convert the gbff into a gff3 using bp_genbank2gff3
Using genome tools, I can validate this gff3 by running
gt gff3validator my.gff
and it tells me it's valid. But when i try and convert this gff to a gtf using either genome tools
gt gff3_to_gtf my.gff)
gffread my.gff3 -T -o my.gtf)
it generates an empty file.
Am i going about the the right way?
Any help is appreciated