CscoreTool: fast Hi-C compartment analysis at high resolution

• DOI: 10.1093/bioinformatics/btx802
• Publication Date: 2017-12-13T04:11:05Z
• Authors: Xiaobin Zheng; Yixian Zheng
• Keywords: 0301 basic medicine; 03 medical and health sciences; Transcription, Genetic; Genomics; Chromatin; Software

Abstract

Summary The genome-wide chromosome conformation capture (Hi-C) has revealed that the eukaryotic genome can be partitioned into A and B compartments that have distinctive chromatin and transcription features. Current Principle Component Analyses (PCA)-based method for the A/B compartment prediction based on Hi-C data requires substantial CPU time and memory. We report the development of a method, CscoreTool, which enables fast and memory-efficient determination of A/B compartments at high resolution even in datasets with low sequencing depth.

Availability and implementation https://github.com/scoutzxb/CscoreTool

Supplementary information Supplementary data are available at Bioinformatics online.