How to interpret RAPD data?

[Diane Stothard]

I attended a meeting this past weekend where the hot topic of conversation was 
exactly your question. We all came to the conclusion that, since RAPD data are 
so inconsistent (even using different machines will give you different 
results!) it is best to decide what experimental conditions you want to use 
(temp, MgCl2, etc) and stick with those conditions for all your RAPDs. If a 
certain set of RAPDs does not respond to these conditions, eliminate them from 
further analysis. As far as scoring faint bands, I think that may also be an 
arbitrary decision on your part. Good luck!