How to get actual alignment % from STAR?
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Entering edit mode
18 months ago
John ▴ 220

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

RNA-Seq R • 429 views
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Entering edit mode
18 months ago

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