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CYZ_Torry edited this page Feb 23, 2026 · 2 revisions

Tutorial: NormDis, Global Folding and Checkerboard Analysis

This repository provides a pipeline for computing the strength of high-order genome architectures, specifically Global Folding and Checkerboard patterns from Hi-C data.

Overview

The analysis pipeline comprises three core computational modules:

  1. NormDis & CorrectMap: For normalizing raw Hi-C contact maps and correcting for assembly artifacts.
  2. Global Folding: For detecting and scoring whole-chromosome folding architectures.
  3. Checkerboard: For calculating chromatin compartmentalization entropy scores.

Citation

Please cite our work when using this tool: (https://doi.org/10.1101/2025.07.05.663309)

Getting Started

The primary entry point is the one_click_pipeline.sh script. Ensure your input data is organized in the correct directory structure as described in the main README.

Directory Tree

A typical project base_path should be structured as follows:

base_path/
├── [species_name_1]/
│   └── sps_mtx/
├── [species_name_2]/
│   └── sps_mtx/
└── parameters.txt

Module Workflow

The typical workflow is: Raw Data → NormDis (Normalization) → CorrectMap (Optional QC) → Checkerboard / Global Folding (Analysis) → Scatter_plot (Visualization).

Navigate to the specific Wiki pages for detailed instructions on each module.

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