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Old 12-05-2012, 03:42 PM   #4
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Location: San Diego, CA, USA

Join Date: Sep 2009
Posts: 438

Depends on what score you are talking about. The MAPQ score from bowtie2 has to do with the uniquness of the alignment and not necessarily the quality of the alignment. You want to look at the AS attribute in the extended attributes of the SAM files. Also read up on this section of the bowtie2 manual:

By default bowtie2 is allowing no mismatches in the seed (22 bases for default end-to-end alignment) and a minimum alignment score of -60.6 (with a max of 0) for 100bp reads. Default penalties are something like -6 for a mismatch at a high quality base an -11 for a length-2 gap. Gaps in reads and reference are scored the same. Specifically you get a -5 for a gap open and -3 for each base. So a length-1 gap is -8, length-2 is -11, etc. So with a min score of about -60 you could have as many as 6 mismatches past the seed or all kinds of combinations of gaps and mismatches. You can control all of those parameters. The min score setting is defined as -0.6 + -0.6*L where L is you read length. If you want to set that value you do so with --min-score L,-0.6,-0.6. So you can figure out what you want your min score to be, like say -40, and work backward from that to figure out what values to put in the setting.
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