Is this formula right to calculate actual alignment percentage of my RNA seq data? I want to find out the reads mapped only to annotated genes, my sample is from Ribosome bound RNA, so I would not have introns, I want to exclude rRNA alignments from the percentage alignment.
Alignment % = Total reads - (N_unmapped - N_multimapping - N_noFeature -N_ambiguous)
I would get these four value from ReadsPerGene.out.tab file. Thanks