1. Download all the files to your folder

Your_folder
├── ME_index
├── Snakefile
├── cluster.json
├── sample2json.py
├── scHiCAR_DNA_18bp_barcode.txt.gz
├── fq  # move your raw fastq files to this folder
│   ├── DNA_example_R1_001.fastq.gz
│   └── DNA_example_R2_001.fastq.gz
└── script
    ├── barcode_hash_v2_ME.py
    ├── fq_barcode_correction_R1_ME.py
    ├── raw_fq_update.py

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 Python packages used in the .py files 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 05_cutME_fq/*_cutME_L001_R*_001.fastq.gz files will be used to generate ATAC fragment files (3_ATAC_fragment) and chromatin contact pair files (4_chromatin_contact).