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Old 02-03-2012, 09:53 AM   #1
Location: Cleveland, OH

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Default General question about TopHat

I am using TopHat for some analyses. The program requires the expected mean of the inner distances of the paired reads as a parameter.

However, why does the program need the expected mean inner distance? How does it use this information?

I could not find this information in the online manual.

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Old 02-03-2012, 03:00 PM   #2
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I think it uses it for flagging reads as "properly paired" in the output BAM/SAM file. There may be other ways it uses it but I don't know about those.
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