I want to calculate RPFs for my Ribo-seq experiments using countReads function from ribosomeProfilingQC. The question: is there any way to take into consideration library type (non-stranded, forward-stranded or rev-stranded and PE or SE)? Like it possible to do, for instance, using featureCounts from Rsubread...
Unfortunately, I didn't find that information in the reference manual.
Thanks in advance,