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Old 12-16-2014, 04:20 PM   #92
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Originally Posted by sdriscoll View Post
So in seal if you use ambig=all then that read (hit) is added to all targets it matched (if there were multiple best matches)?
That's correct.
Or say...what happens when a read can match one sequence with 20 kmers and a second with 18 kmers?
Seal will only consider something ambiguous if it matches multiple sequences with the same number of kmers, which is also to the highest number. However, I could add a flag that changes it to allow any number of kmers.
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