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

Join Date: Oct 2013
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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?
KlChen is offline   Reply With Quote

bowtie, multiple hits, order

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