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Unique mapped reads #81

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Hongxiang2023 opened this issue May 10, 2022 · 1 comment

Hongxiang2023 commented May 10, 2022

Hi,

I'm just curious how the unique mapped reads are counted? Is it using the mapping quality or XA and SA tag to filter out the reads?
Thank you!!

Owner

brentp commented May 10, 2022

Hi, it uses the sam flag to determine primary and it only counts primary, not secondary or supplemental reads.

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