Design of the Experiment

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This section provides a detailed explanation of the design.csv input format for the three working modes of dcHiChIP.

Case 1: Only HiChIP raw FASTQ files (no ChIP-seq input)

Use this format when you do not have ChIP-seq data (neither raw nor peak files).

id	sample	hichip_r1	hichip_r2	chipseq_r1	chipseq_r2	narrowpeak
S-1	S1	./hichip/SAMPLE1_R1.fastq.gz	./hichip/SAMPLE1_R2.fastq.gz
S-2	S1	./hichip/SAMPLE2_R1.fastq.gz	./hichip/SAMPLE2_R2.fastq.gz

Notes:

• The last column (chipseq) & (narrowpeak) must be left empty.
• Pseudo-ChIP-seq peaks will be automatically generated from the HiChIP data.

Case 2: HiChIP FASTQ + processed ChIP-seq peak files (narrowPeak)

Use this format when you have pre-processed ChIP-seq peak files in narrowPeak format.

id	sample	hichip_r1	hichip_r2	chipseq_r1	chipseq_r2	narrowpeak
S-1	S1	./hichip/SAMPLE1_R1.fastq.gz	./hichip/SAMPLE1_R2.fastq.gz			./chip/SAMPLE1.narrowpeak
S-2	S1	./hichip/SAMPLE2_R1.fastq.gz	./hichip/SAMPLE2_R2.fastq.gz			./chip/SAMPLE2.narrowpeak

Notes:

• Ensure peak files are in BED6+4 format.
• Chromosome names must follow the chrX naming convention (e.g., chr1, chr21).

Case 3: HiChIP FASTQ + raw ChIP-seq FASTQ files (needs peak calling)

Use this format when you have raw ChIP-seq data and wish to process it within the pipeline.

id	sample	hichip_r1	hichip_r2	chipseq_r1	chipseq_r2	narrowpeak
S-1	S1	./hichip/SAMPLE1_R1.fastq.gz	./hichip/SAMPLE1_R2.fastq.gz	./chipseq/SAMPLE1_R1.fastq.gz	./chipseq/SAMPLE1_R2.fastq.gz
S-2	S1	./hichip/SAMPLE2_R1.fastq.gz	./hichip/SAMPLE2_R2.fastq.gz	./chipseq/SAMPLE2_R1.fastq.gz	./chipseq/SAMPLE2_R1.fastq.gz

Notes:

• ChIP-seq input files must correspond to the same sample and replicate scheme.
• Peak calling will be automatically performed using MACS3.

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Each mode triggers a distinct branch of the pipeline, ensuring flexible integration based on the type and availability of ChIP-seq data.