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CLI Usagechr3d bulk-hic

chr3d bulk-hic

chr3d bulk-hic [OPTIONS]

Run the complete bulk Hi-C pipeline for a single sample.

Examples

Basic Example

chr3d bulk-hic \
    --r1 sample_R1.fastq.gz \
    --r2 sample_R2.fastq.gz \
    --genome /data/genomes/hg38.fa \
    --chrom-sizes /data/genomes/hg38.chrom.sizes \
    --output-dir ./results/my_sample \
    --sample-id my_sample

Advanced Example

chr3d bulk-hic \
    --r1 sample_R1.fastq.gz \
    --r2 sample_R2.fastq.gz \
    --genome /data/genomes/hg38.fa \
    --chrom-sizes /data/genomes/hg38.chrom.sizes \
    --output-dir ./results/my_sample \
    --sample-id my_sample \
    --restriction-enzyme MboI \
    --threads 24 \
    --resolutions 1000,5000,10000,25000,50000,100000 \
    --tad-windows 30000,50000,100000,200000,500000,1000000 \
    --loop-fdr 0.05 \
    --compartment-phasing-track /data/annotations/gene_density.bed \
    --keep-intermediates \
    --verbose

Resume from Pairs Step

chr3d bulk-hic \
    --genome /data/genomes/hg38.fa \
    --chrom-sizes /data/genomes/hg38.chrom.sizes \
    --output-dir ./results/my_sample \
    --start-from 3

Pipeline Steps

  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 → .cool + .mcool
  5. TADs — insulation score calling (optional)
  6. Loops — Hi-C loop calling (optional)
  7. Compartments — A/B compartment calling (optional)

Output Layout

<output-dir>/
├── aligned/          sorted BAM + flagstat
├── pairs/            .pairs.gz files
├── matrices/         .cool + .mcool
├── tads/             TAD calls (if enabled)
├── loops/            Loop calls (if enabled)
└── compartments/     Compartment calls (if enabled)

Arguments

Required Arguments

ArgumentDescription
--genome PATHBWA-indexed genome FASTA (e.g., /ref/hg38.fa)
--chrom-sizes PATHChromosome sizes file (e.g., hg38.chrom.sizes)
--output-dir DIROutput directory (created if it does not exist)

Input Arguments

ArgumentDefaultDescription
--r1 FASTQ—R1 FASTQ file (required unless --start-from > 1)
--r2 FASTQ—R2 FASTQ file (required unless --start-from > 1)
--sample-id STRsampleSample identifier used in output file names

Processing Arguments

ArgumentDefaultDescription
--threads N4Number of CPU threads
--splits N0Split FASTQ into N chunks for parallel alignment; 0 = no splitting
--assembly NAMEhg38Genome assembly name written into .cool metadata

Filtering Arguments

ArgumentDefaultDescription
--min-mapq INT30Minimum BWA mapping quality
--min-distance BP1000Minimum pair distance in bp
--resolutions CSV1000,5000,10000Comma-separated list of matrix resolutions in bp

TAD Calling Arguments

ArgumentDefaultDescription
--no-tads—Skip TAD / insulation score calling
--tad-windows CSV—Comma-separated insulation window sizes in bp (default: 30000,50000,100000,200000,500000,1000000)

Loop Calling Arguments

ArgumentDefaultDescription
--no-loops—Skip Hi-C loop calling
--loop-fdr FLOAT0.1FDR threshold for loop significance

Restriction Enzyme Arguments

ArgumentDefaultDescription
--restriction-enzyme NAME_OR_SITE—Restriction enzyme name (HindIII, DpnII, MboI, BglII, Arima) or recognition site with cut position (e.g., A^AGCTT). Use "none" for DNase Hi-C / Micro-C
--fragment-bed BED—Pre-computed restriction fragment BED file. If provided with --restriction-enzyme, skips auto-generation

Compartment Calling Arguments

ArgumentDefaultDescription
--no-compartments—Skip A/B compartment calling
--compartment-phasing-track BED—BED file (chrom,start,end,value) to orient E1 sign, e.g., gene density track

Output Control

ArgumentDescription
--keep-intermediatesKeep intermediate BAM / pairs files (default: delete them)

Resume Arguments

ArgumentDefaultDescription
--start-from STEP1Resume from step N (1-7). 1=alignment, 2=SAM/BAM, 3=pairs, 4=matrix, 5=TADs, 6=loops, 7=compartments

Logging Arguments

ArgumentDescription
-v, --verboseEnable DEBUG-level logging
--log-file FILEWrite log to FILE in addition to stdout
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