I have run htseq to obtain read counts for contiges. Though I use the same gtf file for each bam file (I have 15 bam files from 15 tissues), htseq output differs for each tissue in terms of the number of contigs being counted. Assume that the gtf file has the information of 15000 contiges. But htseq output for each tissue has a different number of contiges. One has the read counts of 12000 contiges, another one 11000, and so on. As I have noticed, no contige has a read count of zero. It seems like htseq has ignored contiges with zero read counts. Why is it? I have used galaxy to run htseq.
Thanks a lot