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Old 07-19-2011, 01:56 PM   #2
kwatts59
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Location: nevada

Join Date: Apr 2011
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First find the number of reads that map at least once. To do this, run bowtie with "-k 1" option. Lets call this number K1.

Then run bowtie with the "-k 2" option. This will report up to two alignments per read. Lets call this number K2.

Subtracting the K1 from K2 gives the number of reads that mapped two or more times. Lets call this number K2p.

To find the number of reads that mapped exactly once, subtract K2p from K1.

To find the number of reads that did not map at all, just subtract K1 from the total number of reads in your sample.
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