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

Sheng-Yao Su1,2,3, I-Hsuan Lu2, Wen-Chih Cheng4

  • 1Taiwan International Graduate Program (TIGP) on Bioinformatics, Academia Sinica, Taipei, Taiwan.

BMC Genomics
|April 4, 2020
PubMed
Summary

The EpiMOLAS framework simplifies whole-genome bisulfite sequencing (WGBS) data analysis. It integrates containerization and web-based tools for efficient processing and reproducible epigenomic research.

Keywords:
DNA methylation data analysisDockerGalaxy platformWGBS pipeline

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Area of Science:

  • Epigenomics
  • Computational Biology
  • Bioinformatics

Background:

  • DNA methylation is a key epigenomic regulator in biological processes.
  • Whole-genome bisulfite sequencing (WGBS) provides single-nucleotide resolution of DNA methylation.
  • WGBS data analysis is complex and presents significant challenges.

Purpose of the Study:

  • To develop an integrated and user-friendly framework for WGBS data analysis.
  • To simplify the process from raw data to downstream analysis.
  • To enable reproducible epigenomic research.

Main Methods:

  • A two-phase approach integrating WGBS data processing and analysis.
  • Development of Galaxy workflows for methylation level calculation and mtable generation.
  • Containerization of the analysis environment using Docker (DocMethyl).
  • A web-based system (EpiMOLAS_web) for data retrieval and analysis linked to gene annotation databases.

Main Results:

  • The DocMethyl Docker image provides a readily deployable computational environment.
  • EpiMOLAS_web facilitates rapid data retrieval and analysis of methylation data.
  • The framework streamlines WGBS data analysis from raw reads to biological insights.

Conclusions:

  • EpiMOLAS is the first framework to combine containerization and web-based systems for comprehensive WGBS analysis.
  • It enhances the ability of researchers to analyze WGBS data and publicly available datasets.
  • The framework promotes reproducible research and deeper understanding of epigenomic mechanisms.