I recently created a tutorial for the Harvard edX PH525.8x Case Study on DNA Methylation Analysis. This tutorial is a step-by-step guide of starting with raw Whole Genome Bisulfite Sequencing (WGBS) reads (SRA or fastq files), apply quality control filters, mapping mapping the filtered reads using Bismark and extracting the methylation calls for downstream analyses such as importing the methylation calls in R to find differently methylated CpGs or differentially methylated regions (see the bsseq R/Bioconductor package for more information).
As an example, we extracted six paired tumor-normal WGBS samples from Ziller et al. (2013) (PMID: 23925113). We have provided the coverage files (only chromosome 22) produced by Bismark in the colonCancerWGBS Github repository for others to use as a data example in R.
I hope others find the tutorial useful for the analysis of their own data!
