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Old 05-12-2015, 12:58 PM   #20
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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Originally Posted by pmiguel View Post
The 4th post in the thread, I actually converted the mass-based/log-linear plot results from the Agilent bioanalyzer chip to a linear, molecule-based plot. This way it can be directly compared to the insert sizes found by mapping the reads-pairs back to the genome from which they came.

The result showed that the shorter amplicons must have clustered preferentially. Really preferentially.

To me this has always suggested there must be some sort of competition for clustering that favors shorter amplicons.
Impressive; I was under the impression that inserts much over 800bp simply would not bridge-amplify. Maybe we should try that approach! Anyway, rather than shorter molecules vastly out-competing longer molecules at all lengths, that could be a more of a case where the rates are fairly similar up to a point (1kbp?) after which longer molecules start failing to form clusters at all (even if there were no short molecules present). I'm just guessing, though.
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