Nested TAD Detection

概要

Facilitates the identification of nested TAD and sub-TAD structures from multi-resolution Hi-C data by streamlining the workflow from raw files to standardized outputs. This skill automates the extraction of chromosome-specific dense matrices from .mcool, .cool, or .hic formats, performs necessary data quality checks, and runs the OnTAD software to generate hierarchical annotation files. It is an essential tool for genomic researchers investigating spatial regulatory architecture, boundary usage, and the enrichment of regulatory elements within inner sub-TAD structures across different cell types or conditions.

主な機能

• Supports automated conversion of .hic files to .mcool for downstream analysis compatibility
• Detects hierarchical TAD and sub-TAD structures using the specialized OnTAD algorithm
• Performs matrix quality control including symmetry checks and contact decay verification
• 2 GitHub stars
• Standardizes raw OnTAD output into BED-like tables and hierarchical annotation files
• Extracts chromosome and resolution-specific dense Hi-C matrices from multi-resolution files

ユースケース

• Comparing TAD hierarchy and boundary sharing between different cell types or experimental conditions
• Investigating whether inner sub-TADs are enriched for active regulatory elements or specific histone marks
• Integrating nested TAD architecture with ChIP-seq, ATAC-seq, or WGBS data to study spatial gene regulation