chr3d hichip


chr3d hichip [OPTIONS]

Run the HiChIP pipeline (align → dedup → MboI purify → background model).

Examples

Basic Example


# First generate fragments, then run HiChIP
chr3d digest -e MboI -o hg38_MboI.bed /data/genomes/hg38.fa
 
chr3d hichip \
    --r1 sample_R1.fastq.gz \
    --r2 sample_R2.fastq.gz \
    --genome /data/genomes/hg38.fa \
    --fragments hg38_MboI.bed \
    --output-dir ./results/hichip \
    --sample-id my_sample

Advanced Example


chr3d hichip \
    --r1 sample_R1.fastq.gz \
    --r2 sample_R2.fastq.gz \
    --genome /data/genomes/hg38.fa \
    --fragments hg38_MboI.bed \
    --output-dir ./results/hichip \
    --sample-id my_sample \
    --threads 48 \
    --n-chunks 12 \
    --min-insert 150 \
    --background-samples 20000 \
    --keep-intermediates \
    --verbose

Pipeline Steps

FASTQ splitting into parallel chunks
BWA MEM -5SP -T0 alignment (per chunk, merged)
BAM → BEDPE + 5’ coordinate deduplication
MboI restriction fragment purification
Background model (randomised PETs, distance decay)

Arguments

Required Arguments

Argument	Description
`--genome FASTA`	BWA-indexed genome FASTA
`--fragments BED`	Restriction fragment BED (e.g., MboI from `chr3d digest`)
`--output-dir DIR`	Output directory

Input Arguments

Argument	Default	Description
`--r1 FASTQ`	—	R1 FASTQ file
`--r2 FASTQ`	—	R2 FASTQ file
`--sample-id STR`	`sample`	Sample identifier

Processing Arguments

Argument	Default	Description
`--threads INT`	`24`	Total CPU threads
`--n-chunks INT`	`6`	Parallel BWA jobs — threads split evenly
`--min-insert INT`	`100`	Min insert size for MboI purification (bp)
`--background-samples INT`	`10000`	Background samples per template for loop calling

Other Arguments

Argument	Description
`--keep-intermediates`	Keep per-chunk FASTQ/BAM files after merge
`--start-from STEP`	Resume from step (1-6)
`-v, --verbose`	Enable DEBUG-level logging
`--log-file FILE`	Write log to FILE