Hi-C TAD Calling & Visualization FAQs

Question 1

What does the Hi-C TAD Calling & Visualization skill do?

Accepted Answer

This skill automates the identification of Topologically Associating Domains (TADs) from Hi-C data files. It handles data conversion, performs statistical TAD calling using HiCExplorer, and generates high-resolution contact maps with boundary overlays for specific genomic regions.

Question 2

What outputs are generated by this process?

Accepted Answer

The skill generates organized project directories containing called TAD boundaries in BED and GFF formats, diagnostic log files, and PDF visualizations showing the Hi-C contact maps with identified TAD boundaries overlayed on the target genomic loci.

Question 3

Can I customize the TAD calling parameters?

Accepted Answer

Yes. The skill allows you to define specific parameters including minimum and maximum window depths, step sizes, multiple testing correction methods (FDR), and significance thresholds to match the specific resolution and quality of your Hi-C data.

Question 4

How does this skill improve a bioinformatics workflow in Claude Code?

Accepted Answer

It streamlines complex command-line workflows into a guided AI interaction. Instead of manually writing HiCExplorer syntax, Claude manages project initialization, parameter validation (like depth and resolution checks), and visualization configuration, reducing errors in 3D genome analysis.

Question 5

Which genomic file formats are supported by this skill?

Accepted Answer

The skill supports .mcool, .cool, and .hic formats. If a user provides a .hic file, the skill automatically handles the conversion to .mcool format to ensure compatibility with downstream analysis tools like HiCExplorer.

Hi-C TAD Calling & Visualization

Hi-C TAD Calling & Visualization

Key Features

Use Cases

Key Features

Use Cases