The combination of DNA bisulfite treatment with high-throughput sequencing technologies has enabled investigation of genome-wide DNA methylation beyond CpG sites and CpG islands. These technologies have opened new avenues to understand the interplay between epigenetic events, chromatin plasticity and gene regulation. However, the processing, managing and mining of this huge volume of data require specialized computational tools and statistical methods that are yet to be standardized. Here, we describe a complete bisulfite sequencing analysis workflow, including recently developed programs, highlighting each of the crucial analysis steps required, i.e. sequencing quality control, reads alignment, methylation scoring, methylation heterogeneity assessment, genomic features annotation, data visualization and determination of differentially methylated cytosines. Moreover, we discuss the limitations of these technologies and considerations to perform suitable analyses.
Swarnaseetha Adusumalli1,#, Mohd Feroz Mohd Omar 1, Richie Soong 1,2 and Touati Benoukraf 1,*
- 1Cancer Science Institute of Singapore, National University of Singapore, Singapore
- 2Department of Pathology, National University Health System, Singapore
- #Current address: Genome Institute of Singapore, A*STAR, Singapore
- *Corresponding author