conversion from .gff3 to .gtf results in empty .gtf file

gpertea / gffread

GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more

MIT License

378 stars 39 forks source link

conversion from .gff3 to .gtf results in empty .gtf file #137

Open jsnoliva opened 2 months ago

jsnoliva commented 2 months ago

Hello,

when i use gffread to convert TE annotation .gff3 to .gtf file, my resulting .gtf turns out to be an empty file. It seems to convert successfully when i convert a gene annotation .gff3 to .gtf still though.

my command: gffread fix_Zm-B73-REFERENCE-NAM-5.0.TE.gff3 -T -o fix_Zm-B73-REFERENCE-NAM-5.0.TE.gtf

jsnoliva commented 2 months ago

when checking the file with gffread B73.PLATINUM.pseudomolecules-v1.fasta.mod.EDTA.TEanno.gff3 -E i get

Command line was: gffread B73.PLATINUM.pseudomolecules-v1.fasta.mod.EDTA.TEanno.gff3 -E .. loaded 0 genomic features from B73.PLATINUM.pseudomolecules-v1.fasta.mod.EDTA.TEanno.gff3