I created a gff3 file from GenBank file containing multiple contigs (using Bioperl 'genbank2gff3.pl' tool) . In order to run HTSeq I removed the ##FASTA section (HTSeq doesn't likes). My gff3 file is missing the headers at the start of the file but HTSeq seems doesn' t mind.
I have a result from HTSeq but I'm not sure I did something wrong.
GFF3 file is attached here: https://docs.google.com/file/d/0B8-ZAuZe8jldNUNhZkdVbV9YQXM/edit?usp=sharing
Thank you for your help.
python -m HTSeq.scripts.count -m intersection-nonempty -t CDS -i ID R_2012_09_17_05_52_53_user_PGM-18-BB_Auto_PGM-18-BB_19_2.sam HPNK.gbf.gff > HPNK_2.counts
Link to genbank2gff3.pl script: