• XR-seq and Damage-seq analysis

Raw XR-seq and Damage-seq datasets are processed using pipeline in here

• TAD calling

TAD calling is performed using Arrowhead with default parameters using script in tad-calling.sh

• 3D modelling

TADs and contact matrices are first processed with 3d-preprocess.sh by following procedure in here. Then Chrom3D used for generating 3D genome models via 3d-model.sh

• Simulated datasets are created with boquila via simulation.sh.

• Downstream analysis

Codes in uv-3d.py is used for analysis of Damage-seq and XR-seq data on produced 3D genome model.