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Old 12-22-2010, 07:02 AM   #2
brentp
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Location: salt lake city, UT

Join Date: Apr 2010
Posts: 72
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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.
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