I recently aligned some sequencing data using STAR against an mm10 prebuilt genome. Afterwards, I sorted and indexed using samtools, and proceeded to generate read counts using htseq-count (and appropriately, an mm10 Ensembl gtf file). But all of my read counts are peculiarly all 0's, classified as no features.
A number of other users have reported the same problem here on BioStars, but their concerns weren't resolved. I have to wonder if my reads failed to align, but a quick look at the bam files in IGV shows many aligned reads. Am I using a faulty mm10 annotation file? Would anyone have suggestions/comments?