Juicebox

Juicebox visualizes Hi-C contact maps and processes Hi-C sequencing data into normalized, multi-resolution contact matrices for analysis of three-dimensional genome architecture.

Key Features:

• Hi-C data processing: Processes raw Hi-C sequence data into normalized contact maps.
• Normalized contact maps: Produces normalized contact matrices suitable for multi-resolution analysis.
• .hic file format: Generates a .hic file that encapsulates compressed contact matrices.
• Terabase-scale support: Handles terabase-scale Hi-C datasets for large-scale genomic studies.
• Structural feature detection: Identifies and annotates structural features such as chromatin loops and domains.

Scientific Applications:

• Three-dimensional genome architecture: Analysis and visualization of genome folding and spatial organization using Hi-C data.
• Chromatin organization and gene regulation: Detection of loops and domains to study relationships between chromatin structure and gene regulation.
• Multi-scale interaction analysis: Examination of genomic interactions across multiple resolutions and scales.

Methodology:

Processes raw Hi-C sequence data into normalized contact maps, generates .hic files containing compressed contact matrices, and identifies/annotates structural features such as loops and domains.