dcHiChIP supports three primary use cases, designed to accommodate the most common experimental scenarios involving HiChIP and ChIP-seq data.
Case 1: HiChIP FASTQ Only
This mode processes raw HiChIP paired-end FASTQ files and performs end-to-end analysis, including alignment, peak calling, loop detection, and 3D modeling.
Case 2: HiChIP FASTQ + Pre-Processed ChIP-Seq Peaks
In this mode, the user provides raw HiChIP FASTQ files along with pre-processed ChIP-seq peaks in narrowPeak format. This bypasses the need for peak calling from HiChIP reads.
Case 3: HiChIP FASTQ + ChIP-Seq FASTQ
This configuration performs joint processing of both HiChIP and ChIP-seq FASTQ files. ChIP-seq reads are aligned, and peaks are called independently to guide HiChIP loop detection.
Each case is automatically detected and managed by the pipeline based on input parameters and file formats provided in the configuration file.