I am trying to analyze human WGBS data using Bismark and methylkit package. I found some discrepancy in %methylation and trying to understand the results.
Can someone help me understand why I see such discrepancy and how to interpret the results? If there are high levels of methylated Cs, shouldn't we expect more methylation at CpG base. Am I interpreting the graph the right way? Is it an issue with methylKit because the total number of nucleotides calculated is not close to the same. Total C's analyzed in Bismark is 1e+e10, whereas the highest number is on the 6e+08 scale for methylkit.