Epi-Flow Documentation

Epi-Flow is a transparent, unified Bash pipeline for Chromatin Analysis from raw FASTQ files to peak calls.

Getting Started

• Design Philosophy
  • The “White Box” Approach
  • A Unified Engine for Multiple Assays
  • Guiding Principles
• Installation & Setup
  • Dependencies
  • Recommended Method: Using Conda / Mamba
  • Alternative: Using HPC Modules
• Preparing Analysis Resources
  • 1. The Reference Genome & Bowtie2 Index (-x)
  • 2. Effective Genome Size (-g)
  • 3. Blacklist Regions (-b)

User Guide

• Pipeline Parameters
  • Required Arguments
  • Paired-End Data
  • Optional Arguments (Tuning & QC)
• Use Cases & Practical Examples
  • Scenario 1: Standard Paired-End ATAC-seq
  • Scenario 2: ChIP-seq for a Transcription Factor (Narrow Peaks)
  • Scenario 3: ChIP-seq for a Broad Histone Mark (Single-End)
  • Scenario 4: CUT&RUN for a Histone Modification
• Interpreting Your Results
  • The Output Directory Structure
  • The Critical First Step: Your QC Dashboard
  • Exploring Your Biological Signal

Advanced Topics

• Beyond the Pipeline: Downstream Analysis Strategies
  • 1. Enhancing Peak Confidence with Input Controls
  • 2. Validating Biological Reproducibility Across Replicates
  • 3. Comparing Conditions: Differential Peak Analysis
  • 4. Refining Your Peak Set: Adjusting Sensitivity
• Support & Contributions
  • Getting Help & Reporting Issues

Indices and tables

• Index

• Search Page