1. Download all the files to your folder

chromatin_contact_folder
├── Snakefile
├── cluster.json
├── config.yaml
├── sample2json.py
├── fq    # This folder contains preprocessed FASTQ files
│   ├── DNA_example_cutME_L001_R1_001.fastq.gz
│   └── DNA_example_cutME_L001_R2_001.fastq.gz
└── script
    ├── extract_barcode_based_on_knee.R
    ├── filter_pairs.py
    ├── read_summary.R

2.Create samples.json file

python3 sample2json.py --fastq_dir fq

3. Run snakemake pipeline (customize -p as needed based on your HPC environment)

Before running Snakemake, please make sure all required R/Python packages used in the .R/.py file under the script folder are installed.

snakemake --latency-wait 60 -p -j 99 --cluster-config cluster.json --cluster "sbatch -p common -J {cluster.job} --mem={cluster.mem} -N 1 -n {threads} -o {cluster.out} -e {cluster.err} " &> log &

The output 04_summary/*.read.summary files summarize contact statistics and serve as QC metrics.

The output 05_filtered/*.dedup.filtered.pairs.gz files can be used in downstream pseudo-bulk or single-cell analysis.