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Call topologically associating domains (TADs) from Hi-C contact matrices using insulation scores and HiCExplorer; outputs boundaries and TAD intervals for downs
Provides step-by-step patterns and code examples to detect topologically associating domains (TADs) from Hi-C contact matrices. It explains how to compute insulation scores (using cooltools), find local minima as boundaries, convert boundaries into TAD intervals, and export results as BED/bedGraph for visualization and downstream analysis. Includes both Python examples (cooler, cooltools, bioframe, matplotlib, pandas) and CLI patterns for HiCExplorer (hicFindTADs).
Use this skill when you have Hi-C contact matrices (cooler/.cool files) and need to identify domain boundaries or compare TAD structure between conditions. Typical scenarios: calling boundaries at multiple scales, generating insulation score tracks for plotting, exporting TAD intervals for overlap/statistical analysis, or producing figures of insulation and boundary locations.
Best suited for agents or workflows that can run Python-based data analysis or shell CLIs with bioinformatics tools installed (Claude Code / Copilot-style agents that can execute Python, or human operators following the instructions).
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