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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 FASTsQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the 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.
Contributors
TADbit is currently developed at the MarciusLab <http://www.marciuslab.org>_ with the contributions of François Serra, David Castillo, Marco Di Stefano, Irene Farabella, Mike Goodstadt and many other members of our Lab
Documentation
TADbit documentation <http://3dgenomes.github.io/TADbit/>_Summary of TADbit classes and functions <https://github.com/3DGenomes/tadbit/blob/master/doc/summary.rst>_If you have any question remaining, we would be happy to answer informally:
.. image:: https://badges.gitter.im/Join%20Chat.svg :alt: Join the chat at https://gitter.im/3DGenomes/tadbit :target: https://gitter.im/3DGenomes/tadbit?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
Check the label FAQ <https://github.com/3DGenomes/TADbit/issues?utf8=%E2%9C%93&q=is%3Aissue+label%3AFAQ+>_ in TADbit issues.
If your question is still unanswered feel free to open a new issue.
Recipe files (Dockerfile <https://docs.docker.com/engine/reference/builder/>_ and
Singularity recipe <https://www.sylabs.io/guides/2.6/user-guide/quick_start.html#build-images-from-scratch>_) to generate containers are
available in the containers folder.
Build the image using the :code:Dockerfile from inside an empty folder with :code:docker build -t tadbit . (~20 minutes)
Once built, run it as :code:docker run tadbit tadbit map -h
This image contains all dependencies for TADbit and also jupyter <http://jupyter.org/>_ .
To run a notebook from inside the docker container run :code:tadbit docker image as::
docker run -it -p 8888:8888 -v /LOCAL_PATH:/mnt tadbit:code:LOCAL_PATH would be for example a local folder with data
(e.g. FASTQs or reference genomes). And :code:/mnt a directory
inside the Docker container where the :code:LOCAL_PATH would be mounted.
From inside docker run::
jupyter notebook --ip 0.0.0.0 --allow-root --NotebookApp.token=''
And finally write the url :code:http://localhost:8888 in your browser.
Note: this can also be done in a single line and running in the background:
::
docker run -d -p 8888:8888 -v /LOCAL_PATH:/mnt tadbit jupyter notebook --ip 0.0.0.0 --allow-root --NotebookApp.token='' > /dev/null &
Build the image using the :code:Singularity from inside an empty folder with :code:sudo singularity build tadbit.simg Singularity (~20 minutes)
Once built, run it as :code:singularity run tadbit.simg
You can also install jupyter inside the Singularity by uncommenting the coresponding line in the recipe file.
Citation
Please, cite this article if you use TADbit.
Serra, F., Baù, D., Goodstadt, M., Castillo, D. Filion, G., & Marti-Renom, M.A. (2017).
Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors.
PLOS Comp Bio 13(7) e1005665. doi:10.1371/journal.pcbi.1005665 <https://doi.org/10.1371/journal.pcbi.1005665>_
In addition to the general citation for the TADbit library, please cite these articles if you used TADbit for:
TADbit has been previously used for modeling genomes and genomic domains. Here is the list of published articles:
TADbit uses other major software packages in biology. Here is the list of their articles:
TADbit training
MuG <http://www.multiscalegenomics.eu/MuGVRE/> workshop: Multi-scale study of 3D Chromatin structure <http://www.multiscalegenomics.eu/MuGVRE/multi-scale-study-of-3d-chromatin-structure/> at the
European Bioinformatics Institute (EMBL-EBI) <https://www.embl.de/training/cco/>_,
Hinxton, Cambridge, (United Kingdom)Chromosomal Conformation course <http://www.crg.eu/en/event/coursescrg-chromosomal-conformation-0> at the
CRG <http://www.crg.eu/en/content/training/>
training programme Barcelona (Spain)3DAROC16 3C-based data analysis and 3D reconstruction of chromatin folding <http://gtpb.igc.gulbenkian.pt/bicourses/3DAROC16/> at the
GTPB <http://gtpb.igc.gulbenkian.pt/bicourses/index.html>
training programme Oeiras (Portugal)Chromosomal Conformation course <http://gtpb.igc.gulbenkian.pt/bicourses/2014/CSDM14/> at the
CRG <http://www.crg.eu/en/content/training/>
training programme Barcelona (Spain)CSDM 2014 <http://gtpb.igc.gulbenkian.pt/bicourses/2014/CSDM14/> at the
GTPB <http://gtpb.igc.gulbenkian.pt/bicourses/index.html>
training programme Oeiras (Portugal)TADbit: Automated Analysis and Three-Dimensional Modeling of Genomic Domains <http://www.eccb14.org/program/tutorials/tadbit> at ECCB14 <http://www.eccb14.org/> Strasbourg (France)CSDM 2013 <http://gtpb.igc.gulbenkian.pt/bicourses/2013/CSDM13/> at the
GTPB <http://gtpb.igc.gulbenkian.pt/bicourses/index.html>
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