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Old 12-21-2010, 06:35 PM   #1
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Location: MA

Join Date: Dec 2010
Posts: 1
Default A question about tophat -g/--max-multihits option

If the --max-multihits option of tophat is set to 1, am I going to get the "best" alignment for the read? For example, will tophat pick the alignment for a read based on the best mapping score or the minimun number of mismatches? I am wondering how tophat works if there are multiple hits and the --max-multihits option is set to 1. Thanks.
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