{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T00:12:43Z","timestamp":1773274363836,"version":"3.50.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1364,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Reliable estimation of the mean fragment length for next-generation short-read sequencing data is an important step in next-generation sequencing analysis pipelines, most notably because of its impact on the accuracy of the enriched regions identified by peak-calling algorithms. Although many peak-calling algorithms include a fragment-length estimation subroutine, the problem has not been adequately solved, as demonstrated by the variability of the estimates returned by different algorithms.<\/jats:p>\n               <jats:p>Results: In this article, we investigate the use of strand cross-correlation to estimate mean fragment length of single-end data and show that traditional estimation approaches have mixed reliability. We observe that the mappability of different parts of the genome can introduce an artificial bias into cross-correlation computations, resulting in incorrect fragment-length estimates. We propose a new approach, called mappability-sensitive cross-correlation (MaSC), which removes this bias and allows for accurate and reliable fragment-length estimation. We analyze the computational complexity of this approach, and evaluate its performance on a test suite of NGS datasets, demonstrating its superiority to traditional cross-correlation analysis.<\/jats:p>\n               <jats:p>Availability: An open-source Perl implementation of our approach is available at http:\/\/www.perkinslab.ca\/Software.html.<\/jats:p>\n               <jats:p>Contact: \u00a0tperkins@ohri.ca<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt001","type":"journal-article","created":{"date-parts":[[2013,1,9]],"date-time":"2013-01-09T19:44:45Z","timestamp":1357760685000},"page":"444-450","source":"Crossref","is-referenced-by-count":27,"title":["MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data"],"prefix":"10.1093","volume":"29","author":[{"given":"Parameswaran","family":"Ramachandran","sequence":"first","affiliation":[{"name":"1 Regenerative Medicine Program, Ottawa Hospital Research Institute, K1H 8L6, Ottawa, Canada and 2Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, K1H 8M5, Ottawa, Canada"},{"name":"1 Regenerative Medicine Program, Ottawa Hospital Research Institute, K1H 8L6, Ottawa, Canada and 2Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, K1H 8M5, Ottawa, Canada"}]},{"given":"Gareth A.","family":"Palidwor","sequence":"additional","affiliation":[{"name":"1 Regenerative Medicine Program, Ottawa Hospital Research Institute, K1H 8L6, Ottawa, Canada and 2Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, K1H 8M5, Ottawa, Canada"}]},{"given":"Christopher J.","family":"Porter","sequence":"additional","affiliation":[{"name":"1 Regenerative Medicine Program, Ottawa Hospital Research Institute, K1H 8L6, Ottawa, Canada and 2Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, K1H 8M5, Ottawa, Canada"}]},{"given":"Theodore J.","family":"Perkins","sequence":"additional","affiliation":[{"name":"1 Regenerative Medicine Program, Ottawa Hospital Research Institute, K1H 8L6, Ottawa, Canada and 2Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, K1H 8M5, Ottawa, Canada"},{"name":"1 Regenerative Medicine Program, Ottawa Hospital Research Institute, K1H 8L6, Ottawa, Canada and 2Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, K1H 8M5, Ottawa, Canada"}]}],"member":"286","published-online":{"date-parts":[[2013,1,7]]},"reference":[{"key":"2023012810254657500_btt001-B1","doi-asserted-by":"crossref","first-page":"D1005","DOI":"10.1093\/nar\/gkq1184","article-title":"NCBI GEO: archive for functional genomics data sets\u201310 years on","volume":"39","author":"Barrett","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012810254657500_btt001-B2","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1186\/1471-2105-12-139","article-title":"Peakranger: a cloud-enabled peak caller for CHIP-seq data","volume":"12","author":"Feng","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2023012810254657500_btt001-B3","doi-asserted-by":"crossref","first-page":"5221","DOI":"10.1093\/nar\/gkn488","article-title":"Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data","volume":"36","author":"Jothi","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012810254657500_btt001-B4","doi-asserted-by":"crossref","first-page":"D493","DOI":"10.1093\/nar\/gkh103","article-title":"The UCSC table browser data retrieval tool","volume":"32","author":"Karolchik","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012810254657500_btt001-B5","doi-asserted-by":"crossref","first-page":"1351","DOI":"10.1038\/nbt.1508","article-title":"Design and analysis of CHIP-seq experiments for DNA-binding proteins","volume":"26","author":"Kharchenko","year":"2008","journal-title":"Nat. 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