Question: How to get actual alignment % from STAR?
gravatar for John
5 months ago by
United States
John210 wrote:


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 file. Thanks

rna-seq R • 158 views
ADD COMMENTlink modified 4 months ago by Biostar ♦♦ 20 • written 5 months ago by John210
gravatar for padwalmk
5 months ago by
padwalmk90 wrote:

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

ADD COMMENTlink written 5 months ago by padwalmk90
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