Hi all, I was hoping I could get some advice from folks that have experience using GeneMarker (or similar software). I am currently working on scoring alleles from 11 microsatellite markers designed specifically for Onychomys leucogaster, using GeneMarker. The actual software is biologist friendly (like they claim) and fairly easy to use; however, I am finding that some markers have more alleles than I expected. I've been told that this is a fairly common problem due to Taq slippage during amplification that may result in multiple PCR products and can be resolved by modifying the panel. I am hesitant to delete alleles without having sound criteria for doing so and was hoping I could get some advice on how to develop this criteria.
Also, I wanted to know whether folks got significantly better results by purifying PCR products prior to fragment analysis, especially those that multiplex loci post-PCR. Thanks, Karla
