Load Nextflow

---

layout: post title: "Hi-C Analysis Using nf-core/hic and nf-core/differentialabundance on MSU HPCC" date: 2025-06-17 author: John Vusich, Leah Terrian, Nicholas Panchy categories: jekyll update

Overview

This guide will show you, step by step, how to analyze Hi-C data using the nf-core/hic pipeline for quality control, alignment, creating contact maps, and calling TADs and compartments.

Key Benefits

• Reproducibility: Community-curated workflows ensure standardized analysis.
• Portability: Run seamlessly on various infrastructures.
• Scalability: Handles datasets of different sizes efficiently.

Prerequisites

• Access to MSU HPCC with a valid ICER account.
• Basic familiarity with the command line.

Note on Directory Variables

On the MSU HPCC:

• $HOME refers to the user’s home directory (/mnt/home/username).
• $SCRATCH refers to the user’s scratch directory, ideal for temporary files and large data processing.

Note on Working Directory

The working directory, where intermediate and temporary files are stored, can be specified using the -w flag when running the pipeline. This helps keep outputs and temporary data organized.

Step-by-Step Tutorial

Part 1: Pre-processing with nf-core/hic

1. Create a Project Directory

Make a new folder for your Hi-C analysis:

mkdir $HOME/hic
cd $HOME/hic

This command creates the directory and moves you into it.

2. Prepare a Sample Sheet

You need to create a file called samplesheet.csv that lists your samples and their FASTQ file paths. Use a text editor (like nano) to create this file:

nano samplesheet.csv

Then, add your sample information in CSV format. For example:

sample,fastq_1,fastq_2
CONTROL_REP1,/path/to/CONTROL_REP1_R1.fastq.gz,/path/to/CONTROL_REP1_R2.fastq.gz
CONTROL_REP2,/path/to/CONTROL_REP2_R1.fastq.gz,/path/to/CONTROL_REP2_R2.fastq.gz
TREATMENT_REP1,/path/to/TREATMENT_REP1_R1.fastq.gz,/path/to/TREATMENT_REP1_R2.fastq.gz
TREATMENT_REP2,/path/to/TREATMENT_REP2_R1.fastq.gz,/path/to/TREATMENT_REP2_R2.fastq.gz

Save the file (in nano, press Ctrl+O then Ctrl+X to exit).

3. Create a Configuration File

Do not type file content directly into the terminal. Use a text editor instead. Create a file named icer.config:

nano icer.config

Paste the following content into the file:

process {
    executor = 'slurm'
}

Save and exit the editor.

4. Prepare the Job Submission Script

Now, create a shell script to run the pipeline. Create a file called run_hic.sh:

nano run_hic.sh

Paste in the following script:

#!/bin/bash --login
#SBATCH --job-name=hic
#SBATCH --time=24:00:00
#SBATCH --mem=4GB
#SBATCH --cpus-per-task=1
#SBATCH --output=hic-%j.out

# Load Nextflow
module purge
module load Nextflow

# Set the paths to the genome files
GENOME_DIR="/mnt/research/common-data/Bio/genomes/Ensembl_GRCm39_mm39" #Example GRCm39
FASTA="$GENOME_DIR/genome.fa" # Example FASTA

# Define the samplesheet, outdir, workdir, and config
SAMPLESHEET="$HOME/hic/samplesheet.csv" # Example path to sample sheet
OUTDIR="$HOME/hic/results" # Example path to results directory
WORKDIR="$SCRATCH/hic/work" # Example path to work directory
CONFIG="$HOME/hic/icer.config" # Example path to icer.config file

# Run the Hi-C analysis
nextflow pull nf-core/hic
nextflow run nf-core/hic -r 2.1.0 -profile singularity -work-dir $WORKDIR -resume \
--input $SAMPLESHEET \
--outdir $OUTDIR \
--fasta $FASTA \
-c $CONFIG

Make edits as needed. Save and close the file.

Hi-C Use case specific parameters

Hi-C digestion protocol:

nextflow run nf-core/hic --input $SAMPLESHEET --outdir $OUTDIR --fasta $FASTA --digestion 'dnpii'

--digestion automatically sets the --restriction_site and --ligation_site parameter according to the restriction enzyme you used. Available keywords are ‘hindiii’, ‘dpnii’, ‘mboi’, ‘arima’.

DNase Hi-C protocol:

nextflow run nf-core/hic --input $SAMPLESHEET --outdir $OUTDIR --fasta $FASTA --dnase --min_cis_dist 1000

Using --dnase mode, all options related to digestion Hi-C are ignored. Using the --min_cis_dist parameter is recommended to remove spurious ligation products.

5. Submit Your Job

Submit your job to SLURM by typing:

sbatch run_hic.sh

This sends your job to the scheduler on the HPCC.

6. Monitor Your Job

Check the status of your job with:

squeue -u $USER

After completion, your output files will be in the results folder inside your hic directory.

Quick Reminders

• Never type file content into the terminal. Always create or edit files using a text editor (like nano).
• Follow each step carefully.
• Visit the nf-core/hic or nf-core/differentialabundance webpage for more detailed instructions and use cases.

Getting Help

If you encounter issues running nf-core/hic on the HPCC, consider these resources:

• nf-core Community: Visit the nf-core website for documentation and support.
• ICER Support: Contact ICER via the MSU ICER support page.
• Slack Channel: Join the nf-core Slack for real-time assistance.
• Nextflow Documentation: See the Nextflow documentation for further details.

---

Conclusion

Using nf-core/hic and nf-core/differentialabundance on the MSU HPCC simplifies the process of Hi-C analysis, including QC, alignment, quantification, and downstream analysis. The combination of Singularity and Nextflow ensures a reproducible and efficient workflow tailored for high-performance computing environments.

---