TAD Calling

TAD Calling algorithms are a set of algorithms which have the task of identification of hierarchical topological domains in Hi-C data. There are several algorithms which are supported by HiCPack such as TADTree, TADbit and etc. You can easily set the TAD Calling algorithm you want to use in data using TAD_ALGORITHM in HiCPack config file. The results of TAD Calling algorithms will saved in tad_results directory. Here are some introductions about some of these algorithms.

TADTree

The above picture is an Overview of TADtree algorithm. Beginning with contact matrix A, TADTree computes the fold-enrichment over background for each pair of positions. For each interval [i,j], TADTree estimates parameters δ(i,j), β(i,j). Next, for each genomic position i we compute the boundary index, a 1D statistic that looks for local shifts in interaction frequency at TAD boundaries. Finally, a dynamic program finds TAD trees that maximize the boundary index and best fit the contact matrix A, then selects an optimal set of TAD trees to form a TAD forest.

TADbit

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.