- 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
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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.