Hi All,

I just started working with methylation (WGBS) data. I have used Bismark and it generated the methylation of Cs and consecutive Gs. I am guessing this Gs methylation is from Cs from other strand (please correct me if I am wrong). My question is should I consider both while reporting the methylation in a region or should I filter only Cs rows and perform the further analysis?

Thanks. 
As you surmised, the "G" is actually the C on the - strand. The methylation of a region should include both strands, unless you know that whatever you're studying is only affected by single-stranded methylation. Note, however that the Cs in a CpG (the C and subsequent G in bismark's files) typically show roughly symmetric/equal methylation ratios, so a common strategy is to simply combine them into CpG-level methylation levels. Bismark likely has a method for doing that (if not, you can do it with MethylDackel).