I want to quantify how much rRNA and mtRNA has been mapped during an RNA-Seq experiment. I have heard of doing this with featureCounts, but haven't seen an exact way to do it.
My guess was to use featureCounts but this only works off of successfully assigned reads, which doesn't answer the mapped reads. So featureCounts won't work, or maybe, because the rRNA would have been identified through featureCounts anyway?
I have seen several examples of this on bioStars and elsewhere, but I don't see how I apply what they did. I can't find any rRNA databases for mm10 (or anything). My alignment is done with STAR.
How can I quantify how much rRNA and mtRNA has been mapped during an RNA-Seq experiment? -DEC