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Old 12-16-2010, 02:44 AM   #11
dariober
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Location: Cambridge, UK

Join Date: May 2010
Posts: 311
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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)
While:
"-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...

Dario
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