chr3d chia-pet


chr3d chia-pet [OPTIONS]

Run the ChIA-PET pipeline (linker filtering → mapping → peak calling → loop calling).

Examples

Basic Example


chr3d chia-pet \
    --r1 sample_R1.fastq.gz \
    --r2 sample_R2.fastq.gz \
    --genome /data/genomes/hg38.fa \
    --linkers ACGCGATATCGCG \
    --output-dir ./results/chiapet \
    --sample-id my_sample

Advanced Example


chr3d chia-pet \
    --r1 sample_R1.fastq.gz \
    --r2 sample_R2.fastq.gz \
    --genome /data/genomes/hg38.fa \
    --linkers ACGCGATATCGCG,CACTGTGGCTGTGTGG \
    --output-dir ./results/chiapet \
    --sample-id my_sample \
    --threads 24 \
    --mapq 30 \
    --min-score 25 \
    --min-tag 18 \
    --max-tag 50 \
    --genome-size hs \
    --qvalue 0.01 \
    --alpha 0.05 \
    --standard-chroms \
    --cytoband /data/annotations/cytoBand_hg38.txt \
    --keep-intermediates \
    --verbose

Pipeline Steps

Linker filtering — parasail SIMD → filtered FASTQ (same-linker PETs)
Mapping — BWA MEM → BAM + BEDPE (deduplicated)
Peak calling — MACS3 → broadPeak / narrowPeak
Background model
- classify_pets → P2P / P2D / D2D PET files
- extract_templates → templates.csv
- NB sampling → templates_with_nb.csv
- p-values → templates_with_pvalues.csv
- FDR correction → significant_loops.csv

Output Layout


<output-dir>/
├── filtered/          per-linker-category FASTQ + merged filtered FASTQ
├── mapped/            BAM, BEDPE, dedup BEDPE + flagstat
├── peaks/             MACS3 broadPeak + summits
├── loops/
│   ├── classified/    P2P / P2D / D2D PET files
│   ├── templates/     templates.csv, NB params, p-values
│   └── results/       significant_loops.csv
└── qc/                pipeline_summary.txt

Arguments

Required Arguments

Argument	Description
`--genome PATH`	BWA-indexed genome FASTA
`--linkers SEQ[,SEQ]`	Comma-separated linker sequence(s) (e.g., `ACGCGATATCGCG`)
`--output-dir DIR`	Output directory

Input Arguments

Argument	Default	Description
`--r1 FASTQ`	—	R1 FASTQ file (required unless `--start-from` > 1)
`--r2 FASTQ`	—	R2 FASTQ file (required unless `--start-from` > 1)
`--sample-id STR`	`sample`	Sample identifier

Linker Filtering Arguments

Argument	Default	Description
`--min-score INT`	`20`	Minimum parasail alignment score
`--min-tag INT`	`15`	Minimum genomic tag length after linker removal
`--max-tag INT`	`40`	Maximum genomic tag length after linker removal

Mapping Arguments

Argument	Default	Description
`--mapq INT`	`30`	Minimum mapping quality
`--threads N`	`4`	CPU threads for BWA / samtools

Peak Calling Arguments

Argument	Default	Description
`--genome-size STR`	`hs`	MACS3 genome size: `hs`, `mm`, or integer
`--qvalue FLOAT`	`0.05`	MACS3 q-value cutoff

Loop Calling Arguments

Argument	Default	Description
`--alpha FLOAT`	`0.05`	FDR significance threshold
`--standard-chroms`	—	Restrict loop calling to chr1-22 + chrX/Y
`--cytoband FILE`	—	UCSC cytoband file for centromere exclusion

Other Arguments

Argument	Description
`--keep-intermediates`	Keep intermediate BAM files
`--start-from STEP`	Resume from step (1-4)
`-v, --verbose`	Enable DEBUG-level logging
`--log-file FILE`	Write log to FILE