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Old 07-19-2011, 10:18 AM   #1
PFS
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Location: USA

Join Date: Mar 2010
Posts: 55
Default Bowtie call to get unique, multi-hits and nonmatching reads

Hello there,

I want to estimate (1) the number of reads that map uniquely (in one place only), (2) the number of reads that map in multiple places and (3) the number of reads that do not map at all.

Is this the correct bowtie call?

-m 1 --un nomatch_reads.txt -- max multihits_reads.txt

Thanks!
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