Using HTSeq-count on a SAM file?

Question

[iannos]

I am trying to use HTSeq-count on a SAM file I generated using HISAT2, however it looks like I need a GFF file? How do I generate one of those? Thanks!

[WouterDeCoster]

You usually download one. Which organism?

Answer 1

[ahmad mousavi]

Hi

For most of known organism you could use Ensemble FTP website it includes DNA sequences and GFF/GTF files. Just search your organism.