EpiMOLAS: an intuitive web-based framework for genome-wide DNA methylation analysis

Abstract

Background: DNA methylation is a crucial epigenomic mechanism in various biological processes. Using wholegenome bisulfite sequencing (WGBS) technology, methylated cytosine sites can be revealed at the single nucleotide level. However, the WGBS data analysis process is usually complicated and challenging. Results: To alleviate the associated difficulties, we integrated the WGBS data processing steps and downstream analysis into a two-phase approach. First, we set up the required tools in Galaxy and developed workflows to calculate the methylation level from raw WGBS data and generate a methylation status summary, the mtable. This computation environment is wrapped into the Docker container image DocMethyl, which allows users to rapidly deploy an executable environment without tedious software installation and library dependency problems. Next, the mtable files were uploaded to the web server EpiMOLAS_web to link with the gene annotation databases that enable rapid data retrieval and analyses. Conclusion: To our knowledge, the EpiMOLAS framework, consisting of DocMethyl and EpiMOLAS_web, is the first approach to include containerization technology and a web-based system for WGBS data analysis from raw data processing to downstream analysis. EpiMOLAS will help users cope with their WGBS data and also conduct reproducible analyses of publicly available data, thereby gaining insights into the mechanisms underlying complex biological phenomenon.

Methods in DNA methylation array dataset analysis: A review

“…The scalability of the methods can range from moderate (done for multiple samples) to high (done for large amounts of samples). Many bioinformatics methods and pipelines, including Bigmelon [17] , EpiScanpy [18] , EpiMOLAS [19] , MADA [20] , AmpliconDesign [21] , COHCAP [22] , Bicycle [23] , and ChAMP [24] , have been developed for analyzing the extent of high throughput methylation dataset produced by the various platforms for conducting epigenome-wide association studies, whose output is in the proclaimed repositories.…”