{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T06:05:58Z","timestamp":1769753158305,"version":"3.49.0"},"reference-count":74,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,9,10]],"date-time":"2024-09-10T00:00:00Z","timestamp":1725926400000},"content-version":"vor","delay-in-days":101,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health, USA","doi-asserted-by":"crossref","award":["R35GM142917"],"award-info":[{"award-number":["R35GM142917"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health, USA","doi-asserted-by":"crossref","award":["U24ES026699"],"award-info":[{"award-number":["U24ES026699"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health, USA","doi-asserted-by":"crossref","award":["R25DA027995"],"award-info":[{"award-number":["R25DA027995"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health, USA","doi-asserted-by":"crossref","award":["R03AG070474"],"award-info":[{"award-number":["R03AG070474"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health, USA","doi-asserted-by":"crossref","award":["R01NS123571"],"award-info":[{"award-number":["R01NS123571"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,9,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Efficient and reliable profiling methods are essential to study epigenetics. Tn5, one of the first identified prokaryotic transposases with high DNA-binding and tagmentation efficiency, is widely adopted in different genomic and epigenomic protocols for high-throughputly exploring the genome and epigenome. Based on Tn5, the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) and the Cleavage Under Targets and Tagmentation (CUT&amp;Tag) were developed to measure chromatin accessibility and detect DNA\u2013protein interactions. These methodologies can be applied to large amounts of biological samples with low-input levels, such as rare tissues, embryos, and sorted single cells. However, fast and proper processing of these epigenomic data has become a bottleneck because massive data production continues to increase quickly. Furthermore, inappropriate data analysis can generate biased or misleading conclusions. Therefore, it is essential to evaluate the performance of Tn5-based ATAC-seq and CUT&amp;Tag data processing bioinformatics tools, many of which were developed mostly for analyzing chromatin immunoprecipitation followed by sequencing (ChIP-seq) data. Here, we conducted a comprehensive benchmarking analysis to evaluate the performance of eight popular software for processing ATAC-seq and CUT&amp;Tag data. We compared the sensitivity, specificity, and peak width distribution for both narrow-type and broad-type peak calling. We also tested the influence of the availability of control IgG input in CUT&amp;Tag data analysis. Finally, we evaluated the differential analysis strategies commonly used for analyzing the CUT&amp;Tag data. Our study provided comprehensive guidance for selecting bioinformatics tools and recommended analysis strategies, which were implemented into Docker\/Singularity images for streamlined data analysis.<\/jats:p>","DOI":"10.1093\/gpbjnl\/qzae054","type":"journal-article","created":{"date-parts":[[2024,9,10]],"date-time":"2024-09-10T17:09:25Z","timestamp":1725988165000},"source":"Crossref","is-referenced-by-count":13,"title":["Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&amp;Tag Data"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-1008-1336","authenticated-orcid":false,"given":"Siyuan","family":"Cheng","sequence":"first","affiliation":[{"name":"Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine , St. Louis, MO 63108,","place":["USA"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2070-2339","authenticated-orcid":false,"given":"Benpeng","family":"Miao","sequence":"additional","affiliation":[{"name":"Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine , St. Louis, MO 63108,","place":["USA"]},{"name":"Department of Genetics, Washington University School of Medicine , St. Louis, MO 63108,","place":["USA"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1650-0555","authenticated-orcid":false,"given":"Tiandao","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine , St. Louis, MO 63108,","place":["USA"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5615-6774","authenticated-orcid":false,"given":"Guoyan","family":"Zhao","sequence":"additional","affiliation":[{"name":"Department of Genetics, Washington University School of Medicine , St. Louis, MO 63108,","place":["USA"]},{"name":"Department of Neurology, Washington University School of Medicine , St. Louis, MO 63108,","place":["USA"]},{"name":"Department of Pathology and Immunology, Washington University School of Medicine , St. Louis, MO 63108,","place":["USA"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2962-5314","authenticated-orcid":false,"given":"Bo","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine , St. Louis, MO 63108,","place":["USA"]}]}],"member":"286","published-online":{"date-parts":[[2024,9,10]]},"reference":[{"key":"2024101004155339100_qzae054-B1","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1016\/j.cell.2007.01.015","article-title":"The role of chromatin during 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