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Old 06-02-2013, 03:16 PM   #2
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Location: Halifax, Nova Scotia

Join Date: Mar 2009
Posts: 381

why don't you first de-multiplex your sequences based on priming sequence (so then you will not have over lapping amplicons in the files) then just trim of the primers separately ?
I dont fully understand your situation so forgive me if I'm misinterpreting.
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