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Old 12-16-2010, 02:10 AM   #10
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Location: Cambridge, UK

Join Date: Sep 2009
Posts: 625

This depends a bit on your application. If you just want to look at mapped positions for peak calling or something similar it is probably not necessary to remove everthing that has another match somewhere else in the genome, albeit with one or a few mismatches. for example you might encounter the case that you get a perfect 50bp match for your sequence of interest, and another match somewhere else which has say 3 mismatches. Using --best you could report the best alignment, however -m 1 would remove the sequence completely as it has more than one valid alignment (even though one has no mismatches and the other one has got 3 mismatches). Reporting the best sequence or a few of them (with the -k <int> option) will probably require some extra filtering afterwards, whereas -m 1 is a quick and safe option for absolutely unique matches.

Just try a few parameters and look at the alignment stats, sequences removed due to -m and so on until you are happy with the outcome.
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