more than 28 million methylation sites?

Question

[ccagg]

Hi,

I am currently doing a whole genome bisulfite sequencing experiment. After running Bismark methylation caller and calculating percent methylation for each unique CpG, I am coming up with more than 46 million sites. I know that there are only 28 million sites in the genome, so I am very confused about my result. I was wondering if anyone had run into a similar issue after using Bismark?

Thanks!

Answer 1

[igor]

A single CpG is actually two Cs if you consider both strands independently. Bismark will report a separate call for each C. Thus, you should expect twice as many sites.