A practical guide for DNase-seq data analysis: from data management to common applications. (4th June 2019)

• Record Type: Journal Article
• Authors: Liu, Yongjing; Fu, Liangyu; Kaufmann, Kerstin; Chen, Dijun; Chen, Ming
• Is Part Of: Briefings in bioinformatics. Volume 20:Number 5(2020)
• Page Start: 1865
• Page End: 1877
• Publication Date: 2019-06-04
• Subjects: DNase-seq -- pipeline -- chromatin accessibility; Genetics -- Data processing -- Periodicals; Molecular biology -- Data processing -- Periodicals; Genomes -- Data processing -- Periodicals; 572.80285
• DOI: 10.1093/bib/bby057
• Languages: English
• ISSNs: 1467-5463

Abstract

Abstract: Deoxyribonuclease I (DNase I)-hypersensitive site sequencing (DNase-seq) has been widely used to determine chromatin accessibility and its underlying regulatory lexicon. However, exploring DNase-seq data requires sophisticated downstream bioinformatics analyses. In this study, we first review computational methods for all of the major steps in DNase-seq data analysis, including experimental design, quality control, read alignment, peak calling, annotation of cis -regulatory elements, genomic footprinting and visualization. The challenges associated with each step are highlighted. Next, we provide a practical guideline and a computational pipeline for DNase-seq data analysis by integrating some of these tools. We also discuss the competing techniques and the potential applications of this pipeline for the analysis of analogous experimental data. Finally, we discuss the integration of DNase-seq with other functional genomics techniques.