I have recently got into an issue! I have been using htseq-count for RNASeq analysis. I was trying one indexed genome along with gtf file for the counting, it was all fine except the gtf file is grouped based on transcripts. As such, I indexed two new genomes (one from ensembl, another is from flybase, just for comparison). Everything was fine, but the last sample (in total of 6) always counted no features with these two new indexed genomes.
I am wondering if anyone would have any idea about this! Many thanks!