Nested TAD Detection from .mcool Using OnTAD

Overview

This skill performs nested TAD (hierarchical TAD/subTAD) detection from Hi-C data using OnTAD, starting from a .mcool, .cool or .hic file.

Main steps include:

Refer to the Inputs & Outputs section to verify required files and output structure.
Inspect the .mcool file to list available resolutions and alway remember to confirm the chromosome name and analysis resolution with the user.
Extract a balanced or raw dense Hi-C matrix for a selected chromosome and resolution from the .mcool file.
Ensure matrix quality (symmetry, no all-zero rows/columns, reasonable contact decay).
Run OnTAD to call TADs and nested TAD structures.
Parse and standardize OnTAD output into BED-like tables and hierarchical annotation files.