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Old 06-23-2011, 01:48 PM   #4
Jon_Keats
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Location: Phoenix, AZ

Join Date: Mar 2010
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I'm assuming you are trying to get the 5' and 3' ends of each RNA species by circularizing the cDNA? Neat idea, definately the weird distribution when mapped to genome will give bwa some problems. You might want to try Tophat instead for the alignment.

For reads that map at multiple locations bwa will report the other potential sites and will randomly select one unless the mate/pair read dictates the location, but even then it should report the alternative options.
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