How do I quantify my amplicons?

We recommend using the Qubit fluorometer for amplicon quantification.

In our experience, we obtain similar concentrations for the different loci and for multiple samples, when using the same DNA input for all PCR reactions. We recommend examining all amplicons on a 1% agarose gel to see whether all amplicons show a similar band intensity. If similar intensities are observed we randomly pick ~3 amplicons for each locus that we quantify using Qubit.