Detect Single-level TAD

Domaincaller is a wrap of the first 2 steps of HiTAD, which can be used as a method to detect single-level domains from genome-wide contact matrix. Similar to HiTAD, it also takes a cool file as input, and then calculates the adaptive DI track and performs Hidden Markov Model (HMM) to predict TAD boundary locations.

Usage

To run domaincaller, just follow the pseudo command below:

$ domaincaller --uri /path/to/the/cool/URI -O test.tad.bed --DI-output test.DIs.bedGraph --removeCache

Type domaincaller or domaincaller -h on your terminal to print detailed help information for each parameter.