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Old 01-06-2016, 01:41 AM   #3
colindaven
Senior Member
 
Location: Germany

Join Date: Oct 2008
Posts: 415
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One point - it looks like you are using bowtie for alignment, which is obsolete for most purposes. Bowtie2 is a much more accurate aligner, and can detect indels. BWA is another great alternative, as is (commercial) Novoalign.
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