[rboettcher]

Originally Posted by feralBiologist

Thanks for this suggestion. Have you checked whether HTSeq-count and featureCounts produce the same results? HTSeq-count supports certain counting models. Basically, the main issue is how to count reads that hit overlapping genes. I chose HTSeq-count because it is written by the author of DESeq and in the above paper has been "approved" also by the authors of edgeR. If featureCounts produces the same results than the switch would be painless but if there are differences than you need to look into the details.

EDIT: I realised that featureCounts is written by the authors of edgeR so it shall be straight-forward to substitute HTSeq-count. Thanks again to rboettcher.

I suggest to have a look a their manuscript on arXiv where the authors made such as comparison. From my experience both tools produce similar results, see http://arxiv.org/abs/1305.3347

EDIT: another nice feature is that fC outputs gene length, so computation of RPKM is straight forward.