dcHiChIP

dcHiChIP is a modular and scalable pipeline for the multi-scale analysis of chromatin architecture from HiChIP data, developed using Nextflow DSL2. It supports different experimental scenarios, handles a wide variety of input formats, and integrates state-of-the-art tools for loop calling, stripe detection, compartment analysis, and 3D genome modelling.

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Key Features

The pipeline includes the following modules:

• Read Alignment & Filtering (BWA, SAMtools, pairtools)
• Peak Calling (MACS3)
• Loop Calling (MAPS)
• Stripe Calling (gStripe)
• Compartment & TAD Analysis (cooltools)
• Motif & Peak Annotation (HOMER, Bioframe)
• Coverage & Correlation Plots (DeepTools)
• 3D Genome Modelling (MultiMM)
• Subcompartment Calling (CALDER)

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Documentation

A complete and interactive documentation is available at: dcHiChIP Documentation

Example Use Cases

dcHiChIP supports three types of input design:

• Case 1: HiChIP-only input → pseudo-ChIP signal
• Case 2: HiChIP + peak files (.narrowPeak) from ChIP-seq
• Case 3: HiChIP + raw ChIP-seq (with inputs) → calls peaks internally

Example datasets and sample designs are provided in the "Working Cases" section of documentation.

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Input Requirements

To run dcHiChIP, you will need:

• Paired-end HiChIP FASTQ files
• Optionally:
  • ChIP-seq FASTQ files (with/without inputs), or
  • Pre-processed .narrowPeak files
• A design CSV describing samples
• BWA index for the reference genome
• Chromosome sizes file
• Genomic features file (e.g., BED gene annotation)

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Quick Start

1. Install Nextflow (>=22.10.1)

   bash
   curl -s https://get.nextflow.io | bash
   

2. Set up a software environment using one of:

• Docker
• Singularity (recommended for HPC)
• Podman
• Shifter
• Charliecloud
• Conda (only as a last resort)

Note - You can chain multiple config profiles, e.g., profile test, docker.

3. Run your own analysis:

nextflow run SFGLab/dcHiChIP \
             -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> \
             --input samplesheet.csv \
             --outdir results

Note -

• Use nf-core/configs to check if your institute already has a config file.
• For Singularity, pre-download images using nf-core download and set a cache directory (NXF_SINGULARITY_CACHEDIR).
• For Conda, set a cache directory (NXF_CONDA_CACHEDIR) to avoid re-installing environments.