🧬 WGBS DMR Workflow (Bismark → methylKit)

A lightweight, reproducible workflow for processing Whole-Genome Bisulfite Sequencing (WGBS) data and performing DMR analysis, designed for epigenomic analysis and downstream integrative/regulatory modeling.

This repo provides a clean and transparent pipeline for:

• ✅ Bisulfite read alignment (Bismark)
• ✅ Deduplication (deduplicate_bismark)
• ✅ Cytosine methylation extraction (bismark_methylation_extractor)
• ✅ DMR calling (methylKit)
• ✅ DMR annotation (GENCODE + CpG islands)
• ✅ Visualization (Manhattan plots)

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📌 Overview

WGBS enables base-resolution DNA methylation measurement genome-wide, but turning raw FASTQs into analysis-ready methylation tables and interpretable DMR results can be tedious and error-prone.

This workflow is intentionally minimal (4 scripts, no heavy framework), but aims to be:

• reproducible (explicit inputs/outputs)
• portable (no hard-coded cluster paths in scripts)
• transparent (each step is a standalone script)
• compatible with downstream epigenomic / multi-omics integration

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🧱 Pipeline Modules

1. Alignment
2. DMR calling
3. Annotation
4. Plot

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📁 Recommended Directory Layout

project/
├── data/                         # input FASTQs (not tracked)
├── refs/                         # reference files (not tracked)
│   ├── gencode.v38.annotation.gtf
│   └── hg38.cpgs.island.txt
├── scripts/                      # pipeline scripts (tracked)
│   ├── 01_alignment.sh
│   ├── 02_dmr_calling.R
│   ├── 03_annotation.R
│   └── 04_plot_manhattan.R
└── results/                      # outputs (not tracked)
    ├── 01_alignment/
    ├── 02_dmr/
    ├── 03_annotation/
    └── 04_plots/


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## 🔧 Requirements

- **Bismark** ≥ v0.22.3  
- **Bowtie2**  
- **samtools**
- **methylKit**  
- Linux environment