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Old 11-06-2011, 09:53 PM   #1
Location: beijing, china

Join Date: Jun 2010
Posts: 36
Default how --mate-inner-dist and --mate-std-dev affect the tophat mapping result

Now I am using tophat version 1.3.2 and my data is paired-end 100bp reads.

My question is : why --mate-inner-dist and --mate-std-dev can affect the tophat hit number? According to my knowledge about tophat, these two parameter should only affect the second column of sam/bam output.

Look forward to your response and thanks in advance
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