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Hi-C Differential Analysis - Usage Guide

Overview

This skill covers comparing Hi-C contact matrices between conditions to identify differential chromatin interactions, compartment switches, and boundary changes.

Prerequisites

pip install cooler cooltools numpy scipy pandas matplotlib statsmodels bioframe

Quick Start

Tell your AI agent what you want to do:

  • "Compare Hi-C between treatment and control"
  • "Find differential contacts"

Example Prompts

Basic Comparison

"Compute log2 fold change between these two Hi-C samples"

"Show differential contact map"

Feature Comparison

"Find compartment switches between conditions"

"Compare TAD boundaries"

Statistics

"Test for significant differential contacts"

"Apply FDR correction to the p-values"

What the Agent Will Do

  1. Load both cooler files
  2. Normalize for sequencing depth
  3. Compute log2 fold change
  4. Test for significance (if replicates)
  5. Visualize differential contacts

Tips

  • Depth normalization - Essential for fair comparison
  • Replicates - Needed for statistical testing
  • Resolution - Match resolution between samples
  • FDR correction - Apply when testing many contacts