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Old 03-10-2015, 07:44 AM   #3
thomasblomquist
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Location: Ohio

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Ditto with the above. Is this before or after adapter and barcode trimming?

In addition: Most fragment analyzers "phorese" under non-denaturing conditions. Library preparation can lead to heterodimerization between non-homologous captured nucleic acid targets (a lot of complementarity on the ends; adapters/sequencing primers etc). The center portion of these heterodimers bulge out 3-dimensionally and phorese at higher SIZES/Times compared to their True 2-D linear length.

Thus, there will be some discrepancy between the fragment library sizing on electrophoresis, the ladder used and your actual insert size.

-Tom
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