Hello, I was wondering if anyone has tried running TopHat with the option max-multihits=1. From the user manual, I would expect only uniquely-mapped reads to appear in the accepted_hits.sam file, however I can usually find several reads appearing more than once. My understanding is that when max-multihits is set to 1, TopHat is supposed to discard mulitply-mapped reads and not consider them further, e.g. when mapping to junctions. Is my understanding correct? If so, any thoughts on why multi-maps are reported in the alignment?
I am using TopHat-1.0.14 with Bowtie-0.12.5.
Thanks.
Bill
I am using TopHat-1.0.14 with Bowtie-0.12.5.
Thanks.
Bill
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