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Old 12-16-2010, 09:08 PM   #12
Location: Beijing

Join Date: Jul 2010
Posts: 33

Originally Posted by dariober View Post
Consider also that if have a read that has 1 match with 0 errors plus, say, 3 additional matches with 1 error than:
"-m 1 --best --strata" will report the match with 0 errors (because the match is unique in the best error stratum)
"-m 1" or "-m 1 --best" will suppress all the alignments and report the read as unmapped.

So "-m 1" without "--best --strata" gives the strongest guarantee that a match is unique, although in my opinion it is too conservative.

Please correct me if I'm wrong...

As the manual said "A stronger form of uniqueness is enforced when -m is specified but --best and --strata are not.", your conclusion is right. It is interesting when you play with "strata". In your case, it is not a real "unique" read since it was mapped to 3 locations, but when you add "best and strata" option, bowtie only looked at the "best basket" and found only one alignment (0 error), then bowtie thought it followed the constraint of "-m 1", and finally reported this alignment in the output. So, for common sense, if you want "unique" read, you should not add "best" and "strata" options with "-m 1" since it will distort the view of bowtie for "valid" alignments.
I dislike the concept of "strata", it is not flexible at all comparing to map/alignment quality. I wonder why bowtie can not output something like "map quality".
One more thing is "unique" read depends on your criteria, the number of mismatch you set also takes an effect on that. In your case, if you set number of mismatch to 0 and m to 1, the latter two alignments are not valid at all, bowtie will report it as a "unique" read; if you set it to 1 and m to 1, without "best and strata" option, bowtie will not report it at all, of course will not think it as a "unique" read also.

Last edited by xinwu; 12-16-2010 at 09:27 PM.
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