chr3d sn-hic

chr3d sn-hic [OPTIONS]

Run the single-nucleus Hi-C pipeline over multiple cells from a manifest file.

Examples

Basic Example

chr3d sn-hic \
    --manifest cells.tsv \
    --genome /data/genomes/hg38.fa \
    --chrom-sizes /data/genomes/hg38.chrom.sizes \
    --output-dir ./results/sn_hic \
    --threads 24

Advanced Example

chr3d sn-hic \
    --manifest cells.tsv \
    --genome /data/genomes/hg38.fa \
    --chrom-sizes /data/genomes/hg38.chrom.sizes \
    --output-dir ./results/sn_hic \
    --threads 24 \
    --min-contacts 5000 \
    --resolutions 1000,5000,10000,25000,50000,100000 \
    --keep-intermediates \
    --verbose

Pipeline Steps

Per-cell (run for EACH cell in the manifest):

1. Alignment — BWA MEM → SAM
2. SAM/BAM — samtools sort/index → sorted BAM + flagstat
3. Pairs — pairtools parse/sort/dedup/filter → .pairs.gz
4. Matrix — cooler cload/zoomify → per-cell .cool

After all cells: 5. Cell QC — Filter cells by min-contacts threshold 6. Pseudobulk — cooler merge passing cells → pseudobulk .cool + .mcool

Manifest Format

Tab-separated file (no header):

cell_id    R1.fastq.gz    R2.fastq.gz

Output Layout

<output-dir>/
├── cells/
│   ├── <cell_id>/
│   │   ├── aligned/     sorted BAM
│   │   ├── pairs/       .pairs.gz
│   │   └── matrices/    per-cell .cool
│   └── ...
├── pseudobulk/          pseudobulk.cool + pseudobulk.mcool
└── qc/                  cell_qc_summary.txt + passing_cells.txt

Arguments

Required Arguments

Processing Arguments

Same as bulk-hic:

• --threads N (default: 4)
• --splits N (default: 0)
• --assembly NAME (default: hg38)
• --min-mapq INT (default: 30)
• --min-distance BP (default: 1000)
• --resolutions CSV (default: 1000,5000,10000)

Cell QC Arguments

Other Arguments