A question about tophat -g/--max-multihits option

[keycard]

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.

[brentp]

i think you need to use -g , not --max-multihits due to a bug in the arg parsing in tophat.
but if you use -g 1, then you will get the best alignment and send -m 1 to bowtie.
this: http://bowtie-bio.sourceforge.net/ma...e-options-best
describes how the "best" is determined. it looks at mismatches, then quality.

[Boel]

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.