So basically, I have a .bam file(cut_L7_1_5.bam) and i installed HTSeq-Count onto my local Galaxy server already.
Now, I wish to run it on my .bam file with this command
"python -m HTSeq.scripts.count [options] <alignment_file> <gff_file>"
To my understanding, <alignment_file> is actually the .bam file itself? What about gff_file?
How can i run them?