I have been working with SSR markers from past one year. The isolation part is over and now I have to run these markers for mapping a population. I have been trying few things. I have done Agarose, Denaturing PAGE and Non denaturing PAGE for a small set of my population. Except for Agarose the other gels are giving pretty good resolution but with few additional bands which can cause troubles while data analysis part. In short can anyone of you suggest me THE BEST way to analyse SSR primers?
Thanks and Regards
Allel detection using SSR primers