Introduction

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 <https://github.com/mirnylab/cooler> matrix format, so has low memory requirements when dealing with high resolution data.

Installation

First install dependencies using conda <https://conda.io/miniconda.html>_::

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

Usage

Check the command-line help by domaincaller [-h].

Citation

.. [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