Has anyone observed that when making paired-end libraries the yield of final PCR product is much less as compared to making single-read libraries? I have made libraries in parallel from the exact same nebulized DNA using both kits (repeated twice, using 2 different paired end kits) with the same result. The concentration of PCR product is more than double in the single read library vs the paired end. I suspect the problem is the PCR step, assuming the efficiency of the polishing/tailing/ligation shouldn't be any different for the two kits. Has anyone tried to optimize the PCR beyond the standard protocol?
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