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Old 12-29-2010, 04:36 AM   #3
Boel
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Location: Stockholm, Sweden

Join Date: Oct 2009
Posts: 62
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I don't believe that is correct that setting --max-multihits to 1 gives you the BEST alignment for the read. According to the tophat manual --max-multihits 1 will trow away all reads that have more than 1 valid alignment. Hence you will get back sam files that only contain the reads that have exactly one alignment if this option is set to 1.

Quote:
Instructs TopHat to allow up to this many alignments to the reference for a given read, and suppresses all alignments for reads with more than this many alignments. The default is 40.
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