CscoreTool: fast Hi-C compartment analysis at high resolution

Bioinformatics
Xiaobin Zheng, Yixian Zheng

Abstract

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. https://github.com/scoutzxb/CscoreTool. xzheng@carnegiescience.edu. Supplementary data are available at Bioinformatics online.

References

Dec 21, 2018·Biophysical Reviews·Koustav PalFrancesco Ferrari
Feb 14, 2019·Nucleus·Youngjo KimYixian Zheng
Aug 29, 2018·Nature Methods·Binbin LaiKeji Zhao
Nov 13, 2019·Nature Methods·Ye Zheng, Sündüz Keleş

Related Concepts

Body Fluid Compartments
Genome
Transcription, Genetic
Determination Aspects
Bio-Informatics
Computer Programs and Programming
Genomics
Sequencing
Chromosomes
Cellular Compartment Analysis

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