Thread: subread
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Old 06-04-2013, 11:27 PM   #8
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Location: San Diego, CA, USA

Join Date: Sep 2009
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Jon it seems there are at least a couple "standard" type things that subread redefines. Their method of identifying reads as multi-mapping reads is slightly off from how other short read aligners define them. This threw me off a little today as I was testing out subread.

You can see how they arrive at the value of 49 in the example you've mentioned - I think that's clear enough - but the terminology is a little confusing. They are measuring from left-most alignment coordinate of mate 1 to left-most alignment coordinate of mate 2 where the "standard" is to measure from right-most alignment coordinate of mate 1 to left-most coordinate of mate 2. I can't guess why they chose to use a kind of non-standard way of specifying this distance but it is a little confusing at first.
/* Shawn Driscoll, Gene Expression Laboratory, Pfaff
Salk Institute for Biological Studies, La Jolla, CA, USA */
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