Hello,

I have been trying to install and run HTSeq-count python package on my windows machine since yesterday. I was able to install HTSeq and run a few of their examples. But when I try to run HTseq-count, it keeps telling me I am mssing a number of other python packages, and this has been going on like a chain reaction.

I was wondering if there is a Bioconductor wrapper or Bioconductor package for HTseq.

I have a BAM file (from RNAseq alignment) and GFF file, and would like to do gene quantification (its a non-human genome).

Any ideas would be appreciated.

Thanks, K

As far as I know, there is no HTSeq wrapper in R, since HTSeq is Python-based. However, there are a few Bioconductor packages that will produce identical counts to what HTSeq-count would produce. These include the summarizeOverlaps function in the GenomicAlignments package, and the featureCounts function in the Rsubread package.

Thank you very much, I will try these out.