TADs Calling with HiCExplorer and Cooltools

Overview

This skill enables comprehensive identification and analysis of topologically associating domains (TADs) from Hi-C data stored in .mcool (or .cool) files. It integrates HiCExplorer for robust TAD calling and visualization capabilities.

Main steps include:

• Refer to the Inputs & Outputs section to verify required files and output structure.
• Data Preparation: Ensure .mcool files are formatted correctly and resolutions are verified.
• Always prompt user for resolution used to call TADs.
• TAD Calling: Use HiCExplorer to call TADs with customizable parameters.
• Always prompt user for target genomic loci for visualization.
• Visualization: Generate contact maps with TAD boundaries overlayed, for specific regions of the genome.

When to use this skill