I am doing a DE analysis of Drosophila, after mapping my fasq file to Drosophila genome with hisat2. I am using htseq-count with the gtf file to get the count table.
In the count table, I have the identifier corresponding to 28S rRNA and 18S rRNA, but it has ZERO counts, that can not be possible.
Why I have zero counts? I know that I have ribosomal sequences in my treatments