I previously ran two variations on the Bismark analysis for our Olympia oyster whole genome bisulfite sequencing data:
I followed this up using the MethylKit R package to identify differentially modified loci (DML), based on differing amounts of coverage (1x, 3x, 5x, & 10x) and percent methylation differences between the two groups of oysters (25%, 50%, & 75%).
See the project wiki for experimental design info).
Both sets of analyses were documented in R Projects:
