Thread: subread
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Old 06-04-2013, 11:46 PM   #9
Jon_Keats
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Location: Phoenix, AZ

Join Date: Mar 2010
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Assuming Wei can confirm that is correct. I actually understand your explanation, so thanks @sdriscoll

So if we were to set it dynamically to include read pairs within 1 standard deviation it would be something like:
(mean insert size) - (1SD) - (Length of Read2) = mindist

Ultimately it would be nice if these values were just learned by the program so they didn't need to be hard coded by the user. Most aligners have moved away from this practice as people don't often know the correct values and it can easily be learned from the actual data.
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