Differential TAD Analysis with HiCExplorer

Overview

This skill identifies differentially interacting TADs between two experimental conditions using HiCExplorer.
It assumes that TADs have already been called for the target condition.

Steps:

1. Normalize Hi-C matrices between conditions. Modify the chromosome name in the .mcool file if not started with "chr".
2. Prepare TAD domains (BED file) of the target sample. Make sure the consistence of the chromosame names between .mcool files and BED files. Modify the chromosome name in the BED file if not consistent with the .mcool file.
3. Perform differential TAD analysis.
4. Visualize the Hi-C contact maps for the target and control conditions.
5. Visualize and interpret significant TAD changes.

When to Use This Skill