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Old 05-12-2015, 07:56 AM   #19
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Location: Purdue University, West Lafayette, Indiana

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Originally Posted by Brian Bushnell View Post

The insert size distribution is fairly interesting for a couple reasons. It looks like the platform can probably handle inserts over 450bp fairly well; there were some short inserts, but they did not overwhelmingly out-compete the long ones. But the flat distribution of the short-insert tail is odd.
About the size distribution of the library vs. size distribution of the amplicons that actually cluster. I created a thread some years ago about a somewhat extreme sample clustered on the MiSeq:

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.

At the much higher clustering concentrations using for the 3000/4000 this process may be exacerbated.

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