Wondering if you could help.
I am analysing methylation in a transgene using bisulfite treatment. I had to use five primer pairs to get the a.1500bp section I needed and I have 10 clones of each primer set from each transgenic line. The sequences from each primer set do overlap and so my question is do I cut out the sequences so that there are no overlapping regions before analysis? I was just wondering because some of these overlapping regions are very large and I'm worried they may skew the results.
The program I am using is Kismeth in case that is important.
Many thanks in advance