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For the absence of an integrated scheme for deep data mining of specific biological issues, here we present ATAC-pipe, an efficient pipeline for general analysis of chromatin accessibility data obtained from ATAC-seq experiments. ATAC-pipe captures information includes not only the quality of original data and genome-wide chromatin accessibility but also signatures of significant differential peaks, transcription factor (TF) occupancy and nucleosome positions around regulatory sites. In addition, ATAC-pipe automatically converts statistic results into intuitive plots at publication quality, such as the read length distribution, heatmaps of sample clustering and cell-type-specific regulatory elements, enriched TF occupancy with motifs footprints and TF-driven regulatory networks. ATAC-pipe provides convenient workflow for researchers to study chromatin accessibility and gene regulation.<\/jats:p><jats:p>Availability https:\/\/github.com\/QuKunLab\/ATAC-pipe<\/jats:p>","DOI":"10.1093\/bib\/bby056","type":"journal-article","created":{"date-parts":[[2018,6,2]],"date-time":"2018-06-02T11:08:11Z","timestamp":1527937691000},"page":"1934-1943","source":"Crossref","is-referenced-by-count":26,"title":["ATAC-pipe: general analysis of genome-wide chromatin accessibility"],"prefix":"10.1093","volume":"20","author":[{"given":"Zuqi","family":"Zuo","sequence":"first","affiliation":[{"name":"Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China"}]},{"given":"Yonghao","family":"Jin","sequence":"additional","affiliation":[{"name":"Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China"}]},{"given":"Wen","family":"Zhang","sequence":"additional","affiliation":[{"name":"Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China"}]},{"given":"Yichen","family":"Lu","sequence":"additional","affiliation":[{"name":"Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China"}]},{"given":"Bin","family":"Li","sequence":"additional","affiliation":[{"name":"Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China"}]},{"given":"Kun","family":"Qu","sequence":"additional","affiliation":[{"name":"Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China"}]}],"member":"286","published-online":{"date-parts":[[2019,6,11]]},"reference":[{"issue":"7280","key":"2020080807563790700_bby056-B1","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1038\/nature08911","article-title":"Chromatin remodelling during development","volume":"463","author":"Ho","year":"2010","journal-title":"Nature"},{"issue":"4","key":"2020080807563790700_bby056-B2","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1038\/nrg2752","article-title":"Chromatin structure and the inheritance of epigenetic information","volume":"11","author":"Margueron","year":"2010","journal-title":"Nat Rev 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