I know there have been a few posts on seqanswers and biostars that asked about how to get uniquely mapped reads.
As Heng Li put it,
and
So I thought I would just use a mapping quality cutoff, say 30, to filter out reads to get uniquely mapped reads.
This is simple for single end reads. I'm not sure how to do it for paired end reads since you have two mapping quality numbers. How should it be done?
As Heng Li put it,
"Uniquely mappable read" is never satisfactorily defined.
Looking at mapping quality is not only the simplest but also the best solution in most cases.
This is simple for single end reads. I'm not sure how to do it for paired end reads since you have two mapping quality numbers. How should it be done?
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