How to get actual alignment % from STAR?

Question

[John]

Hi

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

Answer 1

[padwalmk]

Hi, You can use MultiQC which gives everything in a very good format.