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Old 03-15-2013, 11:24 AM   #2
kcchan
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Location: USA

Join Date: Jul 2012
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How much library are you getting with 10 cycles of PCR? 100ng of DNA should get you plenty of library for sequencing. You should double check your upstream steps to ensure everything is working efficiently, especially the adapter ligation.

If you're running the cBot instruments internally, there are also tricks to load your samples starting with less than 1nM of DNA library.

Another question is how you're determining the duplication rate? Some programs such as fastqc do not accurately determine the duplication rate.
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