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
that's funny chat to discuss ideas :)
I was interested in using TADbit. I was wondering if there was a sort of start-to-finish script where we could access the full functionality of TADbit, sort of like a template for processing samples.
there is such a script for the detection of TADs and modeling part (model_and_analyze.py in the script folder. This script should also be in your PATH if you installed TADbit). There are not yet any script for the mapping of NGS reads, and the generation of interactions matrices.
... @scriscio sorry for the delay in answering, my notifications were turned off :(
Can TADbit do a whole genome modeling?
Hi @Bob-Yeah , if you're thinking on a human-size genome. no :)
One more question: why do you use "scorei=eqvsi×dRMSDi/max(dRMSD)/(RMSDi/max(RMSD)) " in "cluster_models" as the score to do model clustering?
This formula is used for two reasons, 1- increase the difference between model 2- and differentiate between mirror models
depending on the type of analysis you may want to differentiate symmetric models into different clusters
Hi, I'm somewhat struggeling in getting TADbit to run. I've successfully installed IMP, also the TADbit installation runs through and "python setup.py check" returns no errors/warnings. However, when I followed some steps in the documentation, I stumbled upon the following import "from pytadbit.imp.CONFIG", which fails because pytadbit does not contain an "imp" module. Do you folks have any idea what might have gone wrong?