How to get the coordinates of TAD

3DGenomes / TADbit

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models

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How to get the coordinates of TAD #324

Open CaiCheng1996 opened 4 years ago

CaiCheng1996 commented 4 years ago

What should I do to get a file containing the coordinates of TAD after I running "find_tad", I can only using "savefig" to get the picture but failed to get the output file with "save_chromosome". Can anyone be so kind to help me?

david-castillo commented 4 years ago

Hi,

The Chromosome object has a set of experiments associated. Each Experiment object has a tads dictionary and a function called write_tad_borders.

Have a look also at the tutorial http://3dgenomes.github.io/TADbit/tutorial/tutorial_8-Compartments_and_TADs_detection.html#tads

Regards

David