Skip to content Skip to footer

Documentation and User Guide for dcHiChIP

Introduction

dcHiChIP workflow

dcHiChIP is a modular and reproducible Nextflow-based pipeline designed for high-throughput analysis of chromatin architecture using HiChIP data. The pipeline supports a wide range of tools for mapping, loop calling, peak annotation, chromatin feature extraction, and 3D modeling.

The pipeline includes integrated modules for:

  • Mapping & filtering of HiChIP/ChIP-seq reads using BWA, SAMtools, and MACS3
  • Loop calling using MAPS and conversion to BEDPE format
  • Feature extraction with cooltools, HOMER, gStripe, and CADLER
  • Multi-resolution compartment and TAD analysis
  • 3D modeling of genome architecture using MultiMM

Working Test Cases

The pipeline supports three fully documented test cases with representative input formats and figure overviews.

👉 Visit Working Test Cases for more.

Design & Sample Sheet

Explore the experimental design principles and detailed sample sheet formats compatible with the pipeline.

👉 Visit Design and Sample Sheet Guide for more.

Module Parameters

Each pipeline module supports customizable parameters such as resolution, CPUs, input formats, and modelling levels.

👉 Visit Module Parameters for full details.

Contact Us

For help, questions, or feedback, feel free to reach out.

👉 Visit Contact Page

Citation

If you use dcHiChIP in your research or publication, please cite the following manuscript (in preparation):

Agarwal, A., Al-Bkhetan, Z., Plewczyński, D. dcHiChIP: A comprehensive Nextflow-based pipeline for Multi-Scale Analysis of Chromatin Architecture from HiChIP Data.

Contributors
AA

ZA