ChIA-PIPE

ChIA-PIPE processes ChIA-PET data to identify and visualize protein-mediated chromatin interactions at base-pair resolution for studying genome architecture and regulatory mechanisms.

Key Features:

• Automated Data Processing: Performs linker filtering, read mapping, peak calling, and loop calling for ChIA-PET datasets.
• Quality Assessment: Produces automated quality control assessments for each dataset.
• Visualization Capabilities: Generates input files compatible with Juicebox and HiGlass and provides a dockerized visualization component for high-resolution exploration of peaks and loops.
• Structural Interpretation: Calls chromatin contact domains, resolves allele-specific peaks and loops, and annotates enhancer-promoter loops.
• Versatility in Data Analysis: Supports analysis of ChIA-PET and related chromatin-mapping data types.

Scientific Applications:

• Genome architecture mapping: Identification and visualization of chromatin contacts to study three-dimensional genome organization.
• Gene regulation analysis: Characterization of protein-mediated chromatin loops to investigate how specific protein factors influence gene expression.
• Allele-specific interaction studies: Resolution of allele-specific peaks and loops to examine allele-dependent regulatory mechanisms.
• Enhancer–promoter annotation: Annotation of enhancer-promoter loops to link regulatory elements with target genes and infer functional regulatory interactions.

Methodology:

Performs linker filtering, read mapping, peak calling, loop calling, automated quality control, calling of chromatin contact domains, resolution of allele-specific peaks and loops, annotation of enhancer-promoter loops, and generation of inputs for Juicebox and HiGlass, with a dockerized visualization component.