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

Join Date: Oct 2009
Posts: 62

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.

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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