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.

License

GNU General Public License (GNU GPL 3)

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of tadbit and load default version of tadbit as

module avail tadbit/ # list available modules
module load tadbit   # load (default) module


If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail tadbit

and choose explicit version you want to use.

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#