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Updated: Jun 13, 2025

Capturing Chromosome Conformation Across Length Scales

Capturing Chromosome Conformation Across Length Scales

Published on: January 20, 2023

CWL-Based Analysis Pipeline for Hi-C Data: From FASTQ Files to Matrices.

Hisashi Miura¹, Rory T Cerbus^2,3, Izumi Noda²

¹Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan. hisashi.miura@riken.jp.

Methods in Molecular Biology (Clifton, N.J.)

|September 16, 2024

Summary

This summary is machine-generated.

A new Common Workflow Language pipeline streamlines Hi-C data analysis, making large-scale 3D genome organization studies more accessible. This facilitates comparative analysis of chromatin interaction data from the 4D Nucleome Data Portal.

Keywords:

3D genome organization Bioinformatics pipeline Common workflow language Hi-C data analysis

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Published on: May 6, 2010

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Last Updated: Jun 13, 2025

Capturing Chromosome Conformation Across Length Scales

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Published on: January 20, 2023

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

Published on: October 14, 2022

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

The Hi-C method has been pivotal in analyzing 3D genome organization for over a decade.
Analysis of large Hi-C datasets, generated using next-generation sequencing (NGS), is computationally intensive.
A growing need exists to simplify Hi-C data processing for broader accessibility and utilization.

Purpose of the Study:

To present a standardized, reproducible, and portable Common Workflow Language (CWL)-based pipeline for Hi-C data analysis.
To enable users to generate Hi-C contact matrices in standard formats (.hic, .mcool) comparable to those in the 4D Nucleome (4DN) Data Portal.
To facilitate comparative genomic analyses by providing a consistent analysis framework.

Main Methods:

Implementation of a CWL-based analysis pipeline within the 4DN Data Portal ecosystem.
Processing of raw FASTQ files to generate standard Hi-C contact matrices.
Utilizing custom scripts, made available on GitHub, for pipeline execution.

Main Results:

The pipeline successfully generates standard Hi-C contact matrices from FASTQ files.
The analyzed data is compatible with the formats available on the 4DN Data Portal, enabling direct comparison.
The CWL pipeline ensures reproducibility and portability of Hi-C data analysis.

Conclusions:

The developed CWL pipeline significantly reduces the computational burden of Hi-C data analysis.
This standardized approach enhances the usability of large Hi-C datasets for research.
The pipeline supports efficient comparative analysis of 3D genome organization across different studies and cell types.