Domaincaller is an implementation of the original Directionality Index (DI) based TAD caller proposed by Dixon et al. [1] Instead of original separate scripts for each stage of the caller, this module provides a convenient command line interface integrating the whole pipeline, including calculating the DI track, performing HMM and post-processing. It supports the .cool matrix format, so has low memory requirements when dealing with high resolution data.
First install dependencies using conda:
conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge conda create -n domaincaller python=3.7.1 cooler=0.8.6 numpy=1.17.2 scipy=1.3.1 pomegranate=0.10.0 networkx=1.11 conda activate domaincaller
Then install the domaincaller using pip:
pip install domaincaller
Check the command-line help by domaincaller [-h].
| [1] | Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 2012, doi: 10.1038/nature11082 |