{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T07:37:16Z","timestamp":1772264236605,"version":"3.50.1"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2018,3,8]],"date-time":"2018-03-08T00:00:00Z","timestamp":1520467200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"Scientific Research","award":["15K18465"],"award-info":[{"award-number":["15K18465"]}]},{"name":"Scientific Research","award":["17H06331"],"award-info":[{"award-number":["17H06331"]}]},{"name":"Scientific Research","award":["15H02369"],"award-info":[{"award-number":["15H02369"]}]},{"name":"Scientific Research","award":["15H05970"],"award-info":[{"award-number":["15H05970"]}]},{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Platform for Drug Discovery, Informatics, and Structural Life Science"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Chromatin immunoprecipitation followed by sequencing (ChIP-seq) can detect read-enriched DNA loci for point-source (e.g. transcription factor binding) and broad-source factors (e.g. various histone modifications). Although numerous quality metrics for ChIP-seq data have been developed, the \u2018peaks\u2019 thus obtained are still difficult to assess with respect to signal-to-noise ratio (S\/N) and the percentage of false positives.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We developed a quality-assessment tool for ChIP-seq data, strand-shift profile (SSP), which quantifies S\/N and peak reliability without peak calling. We validated SSP in-depth using \u2009\u2265\u20091000 publicly available ChIP-seq datasets along with virtual data to demonstrate that SSP provides a quantifiable and sensitive score to different S\/Ns for both point- and broad-source factors, which can be standardized across diverse cell types and read depths. SSP also provides an effective criterion to judge whether a specific normalization or a rejection is required for each sample, which cannot be estimated by quality metrics currently available. Finally, we show that \u2018hidden-duplicate reads\u2019 cause aberrantly high S\/Ns, and SSP provides an additional metric to avoid them, which can also contribute to estimation of peak mode (point- or broad-source) of samples.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>SSP is open source software written in C++\u2009and can be downloaded at https:\/\/github.com\/rnakato\/SSP.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty137","type":"journal-article","created":{"date-parts":[[2018,3,7]],"date-time":"2018-03-07T07:09:10Z","timestamp":1520406550000},"page":"2356-2363","source":"Crossref","is-referenced-by-count":28,"title":["Sensitive and robust assessment of ChIP-seq read distribution using a strand-shift profile"],"prefix":"10.1093","volume":"34","author":[{"given":"Ryuichiro","family":"Nakato","sequence":"first","affiliation":[{"name":"Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1\u20131\u20131 Yayoi, Bunkyo-Ku, Tokyo, Japan"}]},{"given":"Katsuhiko","family":"Shirahige","sequence":"additional","affiliation":[{"name":"Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1\u20131\u20131 Yayoi, Bunkyo-Ku, Tokyo, Japan"}]}],"member":"286","published-online":{"date-parts":[[2018,3,8]]},"reference":[{"key":"2023012712583718100_bty137-B1","doi-asserted-by":"crossref","first-page":"e72.","DOI":"10.1093\/nar\/gks001","article-title":"Summarizing and correcting the GC content bias in high-throughput sequencing","volume":"40","author":"Benjamini","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023012712583718100_bty137-B2","doi-asserted-by":"crossref","first-page":"75.","DOI":"10.3389\/fgene.2014.00075","article-title":"Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data","volume":"5","author":"Carroll","year":"2014","journal-title":"Front. 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