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amaer 10-26-2009 02:50 PM

SOAP2 and gapped alignments
Has anybody used SOAP2 with gapped alignments? If yes, what did you specify in parameters?

We recently got a Linux box and installed SOAP2 on it, the purpose of that being to do gapped alignments on Solexa data. I have tried, but I never got back gapped alignments, only 1 or 2 mismatches.

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