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