I am using eXpress to quantify gene expression by FPKM counts on a database with all genes of one Drosophila species
I would like to look at the expression of Y-linked genes in this species (that have only 1 copy in the entire genome) across many tissues. The point is that all genes were in principle correctly analysed, but two Y-linked genes that I known they are transcribed (by transcriptome assembly) show 0.00 as result in the FPKM count.
I have already checked for all possible troubles I could have made, but I don't understand why these strange results.
Also, the .BAM file that eXpress worked against the reference fasta was explored on the IGV and I saw the RNA-seq reads of these two Y chromosome genes.
Do you known what can be wrong in my data or in the eXpress software?
Thanks a lot for this support!!!