cLoops2: a full-stack comprehensive analytical tool for chromatin interactions

被引：21

作者：

Cao, Yaqiang ^{[1
]}

Liu, Shuai ^{[1
]}

Ren, Gang ^{[1
]}

Tang, Qingsong ^{[1
]}

Zhao, Keji ^{[1
]}

机构：

[1] NHLBI, Lab Epigenome Biol, Syst Biol Ctr, NIH, Bethesda, MD 20892 USA

来源：

NUCLEIC ACIDS RESEARCH | 2022年 / 50卷 / 01期

关键词：

READ ALIGNMENT; GENOME; LOOPS; DNA; ASSOCIATION; SEQ; VISUALIZATION; PRINCIPLES; REGULATOR; EFFICIENT;

D O I：

10.1093/nar/gkab1233

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Investigating chromatin interactions between regulatory regions such as enhancer and promoter elements is vital for understanding the regulation of gene expression. Compared to Hi-C and its variants, the emerging 3D mapping technologies focusing on enriched signals, such as TrAC-looping, reduce the sequencing cost and provide higher interaction resolution for cis-regulatory elements. A robust pipeline is needed for the comprehensive interpretation of these data, especially for loop-centric analysis. Therefore, we have developed a new versatile tool named cLoops2 for the full-stack analysis of these 3D chromatin interaction data. cLoops2 consists of core modules for peak-calling, loop-calling, differentially enriched loops calling and loops annotation. It also contains multiple modules for interaction resolution estimation, data similarity estimation, features quantification, feature aggregation analysis, and visualization. cLoops2 with documentation and example data are open source and freely available at GitHub: https://github.com/KejiZhaoLab/cLoops2.

引用

页码：57 / 71

页数：15

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