Learning Objetives

In this course, participants will learn to use TADbit tools, a wraper to the TADbit python library designed and developed to manage all the dimensionalities of the Hi-C data. Compared to previous 3DAROC courses, this course we will lower the learning curve and provide means to analyze 3C-based data using only command tools. So, if you know how run a command line in linux, you can learn and use TADbit tools. The tutorials will evolve around:

  • 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 tools 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 Jupyter use, graduate level in Life Sciences. All hands-on will be given at command-line tool (experienced users will be given pointers for python scripting TADbit).


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