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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.<\/jats:p>","DOI":"10.1093\/bib\/bby057","type":"journal-article","created":{"date-parts":[[2018,6,13]],"date-time":"2018-06-13T11:10:33Z","timestamp":1528888233000},"page":"1865-1877","source":"Crossref","is-referenced-by-count":15,"title":["A practical guide for DNase-seq data analysis: from data management to common applications"],"prefix":"10.1093","volume":"20","author":[{"given":"Yongjing","family":"Liu","sequence":"first","affiliation":[{"name":"Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liangyu","family":"Fu","sequence":"additional","affiliation":[{"name":"Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universit\u00e4t zu Berlin, Berlin 10115, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kerstin","family":"Kaufmann","sequence":"additional","affiliation":[{"name":"Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universit\u00e4t zu Berlin, Berlin 10115, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dijun","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ming","family":"Chen","sequence":"additional","affiliation":[{"name":"Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universit\u00e4t zu Berlin, Berlin 10115, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,6,4]]},"reference":[{"issue":"4256","key":"2020080807564354800_bby057-B1","doi-asserted-by":"crossref","first-page":"848","DOI":"10.1126\/science.948749","article-title":"Chromosomal subunits in active genes have an altered conformation","volume":"193","author":"Weintraub","year":"1976","journal-title":"Science"},{"issue":"3 Pt 2","key":"2020080807564354800_bby057-B2","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1016\/0092-8674(81)90381-0","article-title":"DNAase I-hypersensitive sites of chromatin","volume":"27","author":"Elgin","year":"1981","journal-title":"Cell"},{"issue":"2","key":"2020080807564354800_bby057-B3","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1016\/j.cell.2007.12.014","article-title":"High-resolution mapping and characterization of open chromatin across the 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