Pooling identical RAD-library PCRs - better for seq of unique fragments?

[RachaelD]

Hi, I have two identical RAD-libraries that I PCR'd in two separate reactions (i.e. final PCR before Illumina seq). One is slightly lower concentration, but I wondered if pooling them at some ratio would help with getting unique RAD-tags in my sample. Does anyone have an opinion on this?

Thanks,
Rachael

[SNPsaurus]

RAD libraries are generally of high complexity, so there probably isn't any advantage in pooling for reducing sampling bias. There could be a little help from pooling in reducing PCR mutations that become amplified, as the same set of mutations are unlikely to have happened in both pools (but I don't think this is typically a problem anyway).

[RachaelD]

Thanks for your thoughts!