I'm working on a population genetics project using newly-developed microsatellite markers (from next-gen sequencing). Using a subset of 96 samples, we have identified 6 variable loci (so far).

My question is: should we screen these 96 samples to eliminate linked loci before we continue, or should we first complete the reactions for all 600 samples and screen the loci at that point?

Thanks for your suggestions,

Tyler

ps - we will continue to test other loci to increase the total number of loci for the project!