puddingstone-nf

A Nextflow pipeline for Hi-C data analysis using cooltools, focusing on expected interactions, insulation scores, eigenvectors, and saddle plots.

Overview

This pipeline processes .mcool files to generate various Hi-C analysis outputs including:

• Expected interaction frequencies
• Insulation scores
• Compartment analysis (eigenvectors)
• Saddle plots

Requirements

• Nextflow (>=21.04.0)
• Docker or Conda
• Input .mcool files

Installation

1. Clone the repository:

git clone https://github.com/gspracklin/puddingstone-nf
cd puddingstone-nf

2. Choose your execution environment:
   • Docker (recommended)
   • Conda environment
   • Singularity

Usage

Basic usage:

nextflow run main.nf -profile docker

Configuration Profiles

• docker: Runs pipeline in Docker container
• standard: Runs pipeline locally
• slurm: Runs pipeline on SLURM cluster
• singularity: Runs pipeline using Singularity

Input Parameters

Configure your analysis in project.yml:

cooler: './path/to/*.mcool'  # Input cooler files

expected:
    expectedOptions: "-p 2"   # Options for expected calculation
    resolution: 20000         # Resolution in base pairs
    window: 100000           # Window size for insulation score
    threads: 4               # Number of threads

Output Directories

• results/expected/: Expected interaction frequencies
• results/insulation/: Insulation scores and boundaries
• results/eigenvectors/: Compartment analysis results
• results/saddle/: Saddle plots

Pipeline Components

1. Expected Interactions

Calculates the expected interaction frequencies as a function of genomic distance.

2. Insulation Analysis

Computes insulation scores and identifies domain boundaries.

3. Eigenvector Analysis

Performs compartment analysis using eigenvector decomposition.

4. Saddle Analysis

Generates saddle plots to visualize compartment strength.

Resource Requirements

• Default: 4 CPUs
• Memory: Scales with input file size
• Storage: ~2-3x input file size

Support

For issues and questions, please open an issue on GitHub.

Citation

If you use this pipeline, please cite:

• cooltools
• This pipeline

License

This project is licensed under MIT License.