The sections in this tutorial steps have to be followed in sequence. At the normalization step, choose the preferred method. Note that A/B compartment analysis can be performed only if the method from Yaffe-Tanay is used, which allows to extract the O/E contact matrix and the Pearson correlation matrix. The method using Hi-Corrector is usually preferred if you have highly deep sequenced data, and it allows both intra- and inter-chromosomal analysis.
All the scripts used in the tutorial are inside the main folder scripts. In this tutorial, all the commands are run supposing that you have downloaded the HiCtool-master folder inside your working directory, otherwise update the paths when you run the commands accordingly.
The explicit-factor correction model of Yaffe and Tanay is applied to normalize and visualize only intra-chromosomal contact data and it takes into account of explicit factors such as fragment length, GC content, mappability score to normalize the data. It has to be used to perform A/B compartment analysis.
The matrix balancing approach of Hi-Corrector is used to normalize and visualize globally intra- and inter-chromosomal contact maps. It does not consider specific factors for normalization and it is faster. Both methods are fine for TAD analysis.