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HiCtool Tutorial (v2.0)

This is a full tutorial of HiCtool. The tutorial steps have to be followed in sequence. At the normalization step, choose the preferred method.

All the scripts used in the tutorial are inside the main folder scripts.

For more information about the Python functions used here check the API documentation.

1. Data preprocessing

2. Data normalization and visualization

The explicit-factor correction model of Yaffe and Tanay is applied to normalize (and visualize) only intra-chromosomal contact data. The matrix balancing approach of Hi-Corrector is used to normalize and visualize globally intra- and inter-chromosomal contact maps.

3. TAD analysis

Supplementary information

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