i tried stringtie by giving the hisat2 output, it was showing error. then i tried converting my refseq .gff to .gtf using gffread. after using gffread i got one output in .gtf format but nothing was written in the file. Help me with this
GFF3 datasets cannot be directly converted to GTF format with the tool you are using.
Instead, obtain a valid GTF file for your target genome. Many are at iGenomes. Please see this prior post for details: https://biostar.usegalaxy.org/p/26873
Thanks, Jen, Galaxy team