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Updated: Oct 31, 2025

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
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The DNA methylation haplotype (mHap) format and mHapTools.

Zhiqiang Zhang1, Yuhao Dan2, Yaochen Xu1

  • 1State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science Chinese Academy of Sciences, Shanghai 200031, China.

Bioinformatics (Oxford, England)
|June 28, 2021
PubMed
Summary
This summary is machine-generated.

We introduce a new DNA methylation haplotype (mHap) format for bisulfite sequencing data. This format significantly reduces file size while preserving crucial methylation information, improving data accessibility.

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Area of Science:

  • Epigenetics
  • Bioinformatics
  • Genomics

Background:

  • Bisulfite sequencing (BS-seq) is the standard for genome-wide DNA methylation analysis at single-nucleotide resolution.
  • Current methods often overlook DNA methylation states within the same DNA fragment (methylation haplotypes or mHaps).

Purpose of the Study:

  • To introduce a novel, efficient DNA mHap format for storing BS-seq data.
  • To develop a tool for converting existing BS-seq data into the mHap format and facilitate data processing.

Main Methods:

  • Development of the mHap data format for DNA methylation haplotypes.
  • Implementation of mHapTools, a command-line tool for BAM/SAM to mHap conversion.
  • Utilizing Tabix for efficient, random access to mHap data.

Main Results:

  • The mHap format reduces BAM file size by 40- to 140-fold.
  • Complete read-level CpG methylation information is retained.
  • Processed all public human reduced representation bisulfite sequencing data into a comprehensive mHap database.

Conclusions:

  • The mHap format offers a significant improvement in storage efficiency for BS-seq data.
  • mHapTools enables easier processing and analysis of DNA methylation haplotype information.
  • The publicly available mHap database provides a valuable resource for epigenetic research.