Question

bowtie2 maximum value of MAPQ

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4.3 years ago

sami ▴ 40

I would like to know the maximum value of MAPQ generated by bowtie2 ?

Thank you

bowtie2 bowtie • 1.8k views

ADD COMMENT • link updated 8 months ago by axol0tl • 0 • written 4.3 years ago by sami ▴ 40

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How is this question different from your previous question: MAPQ mapping quality ? Did the links in the answer to that question not address this question?

ADD REPLY • link 4.3 years ago by Ram 44k

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I would like to know the maximum value of MAPQ using bowtie2 not the best value of MAPQ.

ADD REPLY • link 4.3 years ago by sami ▴ 40

score 2 · Answer 1 · 2020-08-14

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4.3 years ago

Dave Carlson ★ 2.0k

As noted in both the sources that RamRS provided in his linked comment, the max MAPQ score that bowtie2 gives is 42. You should be able to demonstrate this for yourself by examining the distribution of MAPQ scores from your own data.

ADD COMMENT • link 4.3 years ago by Dave Carlson ★ 2.0k

score 0 · Answer 2 · 2024-03-25

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8 months ago

axol0tl • 0

From https://github.com/BenLangmead/bowtie2/issues/357 :

44 is the max for local mode and 42 for end-to-end. You can check unique.h:335 for more information on MAPQ calculations in local mode.

ADD COMMENT • link 8 months ago by axol0tl • 0