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Old 03-07-2017, 09:13 PM   #10
Location: CA

Join Date: Jul 2013
Posts: 74

Are you sure they subtracted the adapter length from the fragment sizes to get the insert sizes (meaning, are you sure they're reporting insert size from the bioanalyzer?)? If the fragments themselves are an average of 600bp with a fairly wide distribution, it wouldn't be surprising if 60% of your reads merged with 150bp PE.

That said, we've (very rarely) had libraries that gave drastically different results between bioanalyzer, fragment analyzer, and tapestation, with the empirical insert size distributions determined after sequencing not agreeing with any of them.
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