GTPB Courses

Learning Objectives and Course Pre-requesites

Learning Objetives

In this course, participants will learn to use TADbit, a software designed and developed to manage all the dimensionalities of the Hi-C data:

  • 1D - Map paired-end sequences to generate Hi-C interaction matrices
  • 2D - Normalize matrices and identify constitutive domains (compartments, TADs)
  • 3D - Generate populations of model structures which reproduce the Hi-C interaction matrices
  • 4D - Compare samples at different time points

Participants can bring specific biological questions and/or their own 3C data to analyze during the course. At the end of the course, participants will be familiar with the TADbit software, and will be able to fully analyze Hi-C data. Note: Although the TADbit software is central in this course, alternative software will be discussed for each part of the analysis.


Course Pre-requisites

Recommended Linux and basic Python programming skills, graduate level in Life Sciences. All hands-on will be given at 3 levels of computational expertise (web platform, command-line tool and python scripting).


TADbit API

This tutorial is associated with a specific version of TADbit, if you wish to reproduce exactly the results in the notebooks you should use the version of TADbit tagged 3DAROC_2018.

To install this version do:

git clone https://github.com/3dgenomes/tadbit
cd tadbit
git checkout tags/3DAROC_2018
sudo python setup.py install


TADbit tools

Most of the tasks of the “core pipeline” can be tunned directly from command line (without any python), using TADbit tool. Have a look to the commands, and the metadata of the results.

For now TADbit tool is not incuded in the general documetation, as it is still “under construction”. Use it carefully, and don’t hesitate to repport any weird behaviour you observe.


Virtual research environment

With small datasets TADbit core pipeline can be runned through a new Virtual Research Environment (VRE), hosted by the MuG project.

This might also be the best place to try TADkit for visualizing genomes in 3D together with interactions matrices and any other genomic track.


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