OnTAD

OnTAD: Optimized Nested TAD Caller for Hi-C Data

OnTAD identifies and characterizes hierarchical topologically associating domains (TADs) from high-throughput chromatin conformation capture (Hi-C) data, enabling analysis of nested chromatin structures and their regulatory organization.

Key Features:

• Hierarchical TAD Identification: Detects nested, multi-level TAD structures from Hi-C contact matrices.
• Boundary Analysis: Analyzes TAD boundaries to assess their roles in chromatin organization and gene regulation.
• Loop Extrusion Model Assessment: Supports evaluation of the loop extrusion model underlying TAD formation.
• Compartmental Domain Analysis: Identifies and characterizes compartmental domains within large-scale chromosomal architecture.

Scientific Applications:

• Chromatin Architecture Analysis: Investigates hierarchical TAD organization, boundary function, and the impact of 3D genome structure on gene regulation and cellular processes.

Methodology:

Processes Hi-C contact matrices to detect regions of enriched interaction frequency corresponding to TADs. Applies parameterized optimization, including penalty values and domain size constraints, with optional log transformation, and outputs identified domains in BED format.