Issue with the sample.count file

[mars188]

Hello,

I ran the following command to get the read counts:

htseq-count -s no -r pos -t CDS -f bam sample2.markdup.bam sample2.map.gtf > sample2.count

The runs smoothly and produces an output file "sample2.count"

When I inspected the sample2.count, it shows gene ids in one column and second column which is supposed to show read counts, contains ALL ZERO in front of every single gene. Only following three rows have a value:

__no_feature | 3302595
__not_aligned | 1464610
__too_low_aQual | 537473

So, I don't know where is the problem. I would really appreciate if someone helps me in this.

Many thanks,

[mars188]

I am still stuck at that step.

Does that mean, my samples has no count or did not align at all?