DupMethAnalyzer

A tool for analyzing DNA methylation differences between segmental duplications in the genome.

Developed by Harris Jeong (2025)

Overview

DupMethAnalyzer examines how DNA methylation patterns differ between highly identical duplicated regions in the genome. It provides detailed methylation comparisons with visualizations to help identify epigenetic differences that may be functionally significant.

Installation

Prerequisites

• Python 3.7 or higher
• minimap2

Install from GitHub

# Clone the repository
git clone https://github.com/hrrsjeong/DupMethAnalyzer.git
cd DupMethAnalyzer

# Install dependencies
pip install -r requirements.txt

Quick Start

python dupmethanalyzer.py --genome genome.fasta --methyl methylation.bed --dups segmental_duplications.bed 

Input Files

DupMethAnalyzer requires three input files:

1. Genome FASTA file (--genome)

   • Contains the reference genome sequences
   • Standard FASTA format with chromosome sequences

2. Methylation BED file (--methyl)

   • Contains DNA methylation information for all CpG loci
   • Format: 5 columns (chromosome, start, end, methylated reads, total reads)
   • Example:

     chr1  10  11  8  10
     chr1  25  26  7  10
     

3. Segmental Duplication BED file (--dups)

   • Contains genomic coordinates of segmental duplicates
   • Format: 6 columns (chrom1, start1, end1, chrom2, start2, end2)
   • Example:

     chr1  1000  2000  chr2  3000  4000
     

Detailed Usage Options

usage: dupmethanalyzer.py [-h] [--genome GENOME] [--methyl METHYL] [--dups DUPS] 
                          [--window WINDOW] [--output OUTPUT] [--minimap2 MINIMAP2]
                          [--threads THREADS] [--minimap2-threads MINIMAP2_THREADS]
                          [--keep-alignments] [--alignment-dir ALIGNMENT_DIR]
                          [--windows-bed WINDOWS_BED] [--version]

Required Arguments

Argument	Description
--genome	Path to genome FASTA file
--methyl	Path to methylation BED file
--dups	Path to segmental duplications BED file

Optional Arguments

Argument	Description	Default
--window	Sliding window size in base pairs	100
--output	Output file path	methyl_diff_output.tsv
--minimap2	Path to minimap2 executable	minimap2
--threads	Number of threads for parallel processing	4
--minimap2-threads	Number of threads per minimap2 process	1
--keep-alignments	Keep alignment files from minimap2	False
--alignment-dir	Directory to store alignment files	alignments
--windows-bed	Output BED file with analyzed windows	None
--version	Show program version and exit

Example Commands

Basic Analysis

python dupmethanalyzer.py --genome genome.fasta --methyl methylation.bed --dups segmental_duplications.bed

Output Files

Main Output

The primary output is a TSV file containing:

• Window coordinates for each duplicated pair
• Sequence identity (overall and window-specific)
• Methylation levels for both regions
• Absolute methylation differences

Additional Outputs

If requested, the tool also generates:

• Windows BED file with all analyzed regions
• Alignment files in PAF format
• Visualization plots:
  • Sequence identity vs. methylation difference
  • Methylation levels comparison
  • Sequence identity distribution

Example Data

We provide example input files to test DupMethAnalyzer:

# Run with example data
cd examples
python ../dupmethanalyzer.py --genome toy_genome.fasta --methyl toy_methylation.bed --dups toy_segmental_dups.bed --window 100

Contact

Harris Jeong
hrrsjeong@gmail.com