differential-tad-analysis

Differential TADs are detected by comparing normalized Hi-C matrices from two conditions using HiCExplorer's hicDifferentialTAD. The workflow identifies statistically significant changes in chromatin domains and exports BED, GFF, and TAD score reports.

Differential TAD analysis requires two Hi-C or mcool files representing target and control conditions, a genome assembly, a chosen resolution, and output directories for normalization, TAD calling, and plots.

Yes, TADs must already be defined for the target condition before detecting differential TADs. The workflow assumes prior TAD calling to detect statistically significant changes between the two conditions.

Yes, the workflow visualizes differential interactions and maps changes onto contact maps. This helps interpret the statistically significant chromatin domain alterations between the two conditions.

Computing differential TADs exports BED, GFF, and TAD score reports. These files capture the normalized matrix comparisons and statistically significant chromatin changes detected by HiCExplorer.

Matrix normalization is required to ensure a fair comparison between two Hi-C conditions. Normalizing the matrices before calling differential TADs prevents bias in detecting statistically significant chromatin changes.