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Old 12-11-2014, 09:54 AM   #1
KlChen
Junior Member
 
Location: Wisconsin, US

Join Date: Oct 2013
Posts: 3
Question The order of multiple hits of a read in Bowtie

Hi, I am using bowtie for the alignment and find that for the reads with multiple hits, the first alignment is more likely (but not always) to be the correct alignment even if the mismatching information is the same.

So I wonder how does bowtie order the multiple hits (if there are) of a specific read?
Do they have some scheme to search the more probable locations first?
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