Question

how much a mapping quality will HISAT2 give to a unique alignment?

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6.1 years ago

Zeason ▴ 10

I just want to find some unique alignment from my sam file with samtools. so i just want to know which figure should be added after samtools view -q ? thank a lot

RNA-Seq • 1.9k views

ADD COMMENT • link updated 5.9 years ago by Biostar 20 • written 6.1 years ago by Zeason ▴ 10

score 0 · Answer 1 · 2018-11-10

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6.1 years ago

h.mon 35k

See HISAT2 MAPQ scoring scheme for a discussion.

ADD COMMENT • link 6.1 years ago by h.mon 35k

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thank you very very much

ADD REPLY • link 6.1 years ago by Zeason ▴ 10