3D Genomics Analysis – Compartment & Insulation Profiling

Workflow Summary

Convert bigWig → bedGraph and bin to 3D resolution

Ensures 1D tracks are on the same bins as .cool matrices.

Compartment & expected tracks

Compute/ingest compartment (eig) tracks and expected contacts per chromosome.

Saddle plots

Use compartment track + expected + .cool to assess compartmentalization strength.

Insulation & pileups

Compute insulation score tracks, then perform pileups across conditions.

Correlations & enrichment

Heatmaps of contact maps, compartment correlations, compartment-strength correlations, insulation-score correlations.

Enrichment of 1D signals within 3D features (A/B, strong/weak compartments, domain borders)

Compartment size distribution

Cumulative plots of compartment/domain sizes across conditions.