Question: htseq-count returning only 0
0
lpb • 0 wrote:
I'm trying to run htseq-count with Bowtie alignments to a bacterial genome. Even though almost 100% of reads aligned to the genome, when I run htseq-count all I get is 0 for every gene. My genome fasta file used for alignment as well as annotation gff were both downloaded from Ensembl and should be correct format. I checked chromosome names in both alignment and annotation as suggested in another post on the subject but that did not fix the problem (there is only one chromosome, so just labeled as "chromosome"). Any other tricks to try? I'm convinced it is just a formatting issue of some sort.