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