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Old 09-10-2013, 08:17 PM   #1
zhouzaiwei
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Default how to report only 1 hit read by bowtie2?

in bowtie1 there is a parameter -m 1 to report only 1 hit read, how to do this in bowtie2?
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Old 09-10-2013, 08:50 PM   #2
a_mt
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In bowtie2 if a read aligns to multiple locations it has XS tag. You can simply use sed to delete lines with this tag, if this is what you wanted.
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Old 09-10-2013, 09:39 PM   #3
zhouzaiwei
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thanks a lot, this is what i wanted.
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