The Basic DNA Methylation (DM) format and DMtools

The Basic DNA methylation (DM) format is a compressed binary indexed DNA methylation format for storing DNA methylation levels with methylation context, strand, coverage, and ID information. Compared with the commonly used file formats for DNA methylation, the storage space of the DM format is reduced by 80%-90%. Besides, based on the DM format file, users can realize fast random access and calculate DNA methylation levels of any chromosome region. Correspondingly, we provided dmtools, a manipulation tool in DM format. The dmtools implements various utilities for post-processing DNA methylation levels with DM format, such as fast and random access, calculation of DNA methylation profile across genes, and differential DNA methylation analysis. Moreover, we also provided a python package pydmtools for processing DM format files.

Installation

• Please download and install the tools (see Install)

The functions you can use dmtools to do:

• DMtools main modules: tools for DNA methylation in dm format, and prepare DM simalar bigwig file for browser.

• bam2dm: Calulate DNA methylation level (ML) across whole genome output dm format.

• Differential analysis: Perform differential analyses with auto defined regions or predefined regions.

• PlotMeth: Plot DNA ML profile, heatmap or boxplot across genes/TEs/etc.

• pydmtools: A python wrapper for dmtools.

Contents

methylation

• Getting started with dmtools
  • Requirements
  • DMtools install
  • python library required for visualization
• dmtools: command line tools
  • Process raw fastq data
    • Description
    • Usage
    • Paramaters
  • Calculate DNA meth from bam
    • Description
    • Usage
    • Paramaters
    • Output files
    • Output file format
  • Format convertion
    • Convert TXT to dm
    • View dm file
    • Convert dm to bigwig
  • Estimate bs conversion rate
    • Description
    • Usage
    • Parameters
  • Calculate DNA meth with dm
    • Calculate DNA methylation for dm file
    • Calculate DNA methylation for regions
    • Calculate DNA methylation for gene body
    • Calculate methylation profile across genes
    • Calculate DNA methylation acorss chromosome
    • Calculate DNA methylation for chromosome
  • Merge or overlap dm files
    • Overlap dm files
    • Merge dm files
  • Manipulate dm format
    • Add zoom level of dm file
    • View DM file header information
• dmplot: plotting from the command line
  • dmplotbasic
  • dmplotcor
    • Description
    • Usage
    • Parameters
  • dmplotheatmap
    • Description
    • Usage and example
    • Parameters
  • dmplotprofile
    • Description
    • Usage and example
    • Parameters
• dmdiff: differential dna methylation
  • DMC or DMR/DMG
  • Usage
    • DMC and DMR detect
    • Obtained hyper、hypo dmc/dmr from dmc/dmr results
  • Parameters
  • Output file
• Requirements
  • gsl library
  • zlib library
• Python API: pydmtools
  • Installation
  • Requirements
  • Usage
    • Load the extension
    • Access the list of chromosomes and their lengths
    • Print the header
    • Compute summary information on a range
    • Retrieve values for individual bases in a range
    • Retrieve all intervals in a range
    • Adding entries to a DM file
    • Close a DM file

While developing dmtools, we continuously strive to create software that fulfills the following criteria:

• new methlation dm format with index can calculate DNA methylation level quickly.

• calculate DNA methylation level based on sorted BAM file for single base or chromosome region and genes.

• enable customized down-stream analyses, espacially with visulization

• generation of highly customizable images (change colours, size, labels, file format, etc.)

Citation

Please cite DMtools as follows:

Zhou Q, Zhou C, Zhu Z, Li G: The Basic DNA Methylation (DM) format and DMtools

Tip

For feature requests or bug reports please open an issue on github.