#31 Paired end reads, bacterial genome

[mpiib1]

Hi, I have paired end reads for a bacterial genome generated from dual RNA-seq of pathogen and host. I was wondering how HTSeq-count counts reads in bacterial genomes when the read pairs fall into different genes (part of an operon)? I would ideally like to count pairs in the same gene as one count and pairs that fall into two genes as one count per gene and was wondering if HTSeq-count can do this.
Thanks!

[Simon Anders]

No, because htseq-count is specifically designed for differential-expression calling, and there, this approach would be sub-optimal. See the documentation to learn how to write a counting script based on HTSeq, which implements your own customized counting rules.