SEQanswers - View Single Post - Bowtie Illumina paired end reads alignment

empyrean · 09-20-2011, 10:51 AM

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

Code:

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?

09-20-2011, 10:51 AM	#4
empyrean Member 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. Code: 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?