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Old 09-20-2011, 09:51 AM   #4
Location: EU

Join Date: Sep 2010
Posts: 52

I should have done that, but now bowtie ran succesfully on my data and gave sam output.

HWI-ST5 1:Y:0:CGAAGT    77      *       0       0       *       *       0       0       ANAANNNNNGGCTCC   ###########   XM:i:0
I got something like the top output in sam format. But i need the information of a read in a pair matches to the reference where as its another pair doesnot. The third column which says * was supposed to be a query_identifier and when i got the reads which are not equal to *, i got all pairs but not singles which map to reference. Can i get this info from bowtie?
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