nested-TAD-detection - Detect Nested TAD Structures from Hi-C Data Using OnTAD
Detects hierarchical (nested) TAD structures from Hi-C contact maps in .cool, .mcool, or .hic format using OnTAD, extracting per-chromosome dense matrices and generating standardized TAD call files.
Tags
Updated: 2026-06-30Capabilities
Typical Inputs
Typical Outputs
What this skill does
- list mcool resolutions
- harmonize chromosome names
- dump chromosome information
- extract dense Hi-C matrix
- run OnTAD TAD detection
- generate BED-like TAD annotation files
Inputs
- Hi-C matrix file (.mcool, .cool, or .hic)
- Chromosome name
- Resolution in bp
- Genome assembly
- Sample name
- Chromosome length
Outputs
- Dense Hi-C matrix file
- OnTAD TAD call file (.tad)
- BED-format TAD annotation file (.bed)
- Log files for matrix extraction and OnTAD run
Requirements
- cooler command-line utilities available in PATH
- OnTAD executable installed and callable
- Python 3.x with scientific Python stack
- MCP tools from cooler-tools, OnTAD-tools, and project-init-tools servers