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Old 06-09-2010, 02:04 PM   #1
jtladner
Junior Member
 
Location: California

Join Date: Feb 2010
Posts: 3
Default Alternative Hits in BWA generated .sam

I am working with Illumina sequences that are about 76 bp long. I have been looking through some .sam files generated by samse after aligning to a reference using bwa. I noticed that many of the reads that contain multiple optimal hits do not have XA tags at the end of the line, while many others do.

I have not noticed any consistent difference between reads that have the XA tag and those that don't. Can anyone offer insight into this?

Jason
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