DNA methylation plays a key role in normal human development and various diseases, including cancer. Coupled with bisulfite treatment, next generation sequencing (RRBS or WGBS) has expanded the scope of DNA methylation studies for the quantitative profiling of DNA methylation of individual CpG loci throughout the genome at a nucleotide resolution. However, analyzing RRBS data is challenging as it needs a significant amount of computational resources and bioinformatics expertise. We developed a comprehensive streamlined pipeline for RRBS data (CSA-RRBS) that integrates read pre-processing, alignment, statistical report of quality, data visualization, and flexible differential methylation analysis between experimental conditions either at single nucleotide resolution (DMC) or with differentially methylated regions (DMRs). Moreover, we also report extensive annotation of the genome region of interest and its overlap with additional genomic features to provide context and perspective to the methylation events. We applied the CSA-RRBS pipeline over two datasets, prostate cell lines (normal and cancer) and a breast cancer patient dataset. The results validate cancer-associated methylation defects and demonstrate that our CSA-RRBS pipeline enables new discoveries about DNA methylation and its role in gene regulation and cancer.