TADbit

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Description

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. Hi-C experiments generate genomic interaction between loci located in the same or in different chromosomes. TADbit is built around the concept of a chromosome, and uses it as a central item to store and compare different Hi-C experiments. The library has been designed to be used by researchers with no expertise in computer science. All-in-one scripts provided in TADbit allow to run the full analysis using one single command line; advanced users may produce their own programs using TADbit as a complementary library.

Category

Others

Availability

Version 0.1 and 0.2.0.44

Licence

GNU General Public License (GNU GPL 3)

Use

module add tadbit-0.2.0.44
tadbit -h

Notice: You should use the full paths to your data files to avoid problems. You should also have that datafiles named properly, with suffix (eg .fastq).

Documentation

https://3dgenomes.github.io/TADbit/

Homepage

https://3dgenomes.github.io/TADbit/index.html#

Program manager

meta@cesnet.cz