CscoreTool: fast Hi-C compartment analysis at high resolution.

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.

Contact

[e-mail].

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Zheng X 

PROVIDER: S-EPMC5925784 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature