I have analysed AFLP data using GeneMapper, and have gone through all the samples checking the peaks that needed checking etc, and I am now ready to export the table to begin further analysis. However, on examining the genotypes table, it is largely filled with 0s and there are hardly any 1s, despite there being lots of peaks visibl on the scans. Does anyone have any idea as to what I have done wrong, or what I need to do to fix this?
In case it is important, I have about 215 alleles, and a few hundred samples (run with 4 different primer combinations, using 2 different dyes).
Any help would be hugely appreciated!!!