How to deal with high % of reads mapped to multiple loci on STAR?
Here is one of my result from STAR alignment.
As you could see, Uniquely mapped reads: 32.37% and % of reads mapped to multiple loci: 60.74%
This sounds not that bad because more than 90% of my reads were aligned well.
However, when I process bam file with featureCounts, Successfully assigned alignments rate is 10.1%
Q1) % of Uniquely mapped reads is 32.37%, and I thought % of successfully assigned alignments will be close to 32.37%,
but only 10.1%. Why is this happening? (I used same annotation GTF file)
Q2) How should I deal with high % of reads mapped to multiple loci?
According to featureCounts manual,
Multi-mapping reads will also be counted. For a multi-mapping read,
all its reported alignments will be counted. The ‘NH’ tag in BAM/SAM
input is used to detect multi-mapping reads.
So if I use -M option then one read may counted more than once? What should I do about it?
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