I am trying to get raw count of mapped read, so I am running htseq-count on tophat accepted hits and my GFF file is Drosophila_melanogaster.BDGP5.77.gtf as I use Dm3 as reference genome for the Tophat. Tophat accepeted hits is 10 000 000 reads ish and the results from Htseq-count is 1 2 __no_feature 8075680 __ambiguous 0 __too_low_aQual 0 __not_aligned 0 __alignment_not_unique 20067133
and no read align for any gene. I kept default setting for htseq-count and check that 3rd column of the GFF was having the exon information and then the gene id was in the good column too
does that mean that I am not using the good GFF file? I use this one because it was named in previous post about which GFF to use with dm3. Or is there something else?