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rcalandrelli committed Mar 29, 2019
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# TAD analysis

This pipeline illustrates the procedure to calculate topologically associated domain (TAD) coordinates and visualize TADs. Topological domain coordinates should be calculated on the normalized data (as we do here) but, if you wish, you can also use this pipeline to calculate TAD coordinates on the observed data. Default species that you can use are human *hg38* and mouse *mm10*. For other species use the specific function arguments (see [API documentation](https://sysbio.ucsd.edu/public/rcalandrelli/HiCtool_API_documentation.pdf).
This pipeline illustrates the procedure to calculate topologically associated domain (TAD) coordinates and visualize TADs. Topological domain coordinates should be calculated on the normalized data (as we do here) but, if you wish, you can also use this pipeline to calculate TAD coordinates on the observed data. Default species that you can use are human *hg38* and mouse *mm10*. For other species use the specific function arguments (see [API documentation](https://sysbio.ucsd.edu/public/rcalandrelli/HiCtool_API_documentation.pdf)).

For more information about the Python functions used here check the [API documentation](https://sysbio.ucsd.edu/public/rcalandrelli/HiCtool_API_documentation.pdf).

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