HiCNAtra

Identification and Utilization of Copy Number Information for Correcting Hi-C Contact Map of Cancer Cell Line. An analytical and visualization tool for CNV discovery and contact map correction of Hi-C/3C-seq data of cancer cell lines. HiCNAtra is a MATLAB-based tool that accepts HDF5 files, the output of hiclib after applying the iterative-mapping technique, as input. HiCNAtra pipeline is divided into three modules: 1) computation of the read depth (RD) signal from Hi-C or 3C-seq reads (RD calculator), 2) RD-based detection of copy number events based on CNAtra approach (CNV caller) and 3) bias correction of chromatin interaction matrix introduced by CNVs and other systematic biases (Contact map corrector)