| MaSC: Mappability-Sensitive Cross-Correlation for Estimating Mean Fragment Length of Single-End Short Read Sequencing Data. | |
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MedLine Citation:
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PMID: 23300135 Owner: NLM Status: Publisher |
Abstract/OtherAbstract:
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MOTIVATION: Reliable estimation of the mean fragment length for nextgeneration short-read sequencing data is an important step in NGS 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. RESULTS: In this paper, 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. AVAILABILITY: An open-source Perl implementation of our approach is available at http://www.perkinslab.ca/Software.html. CONTACT: tperkins@ohri.ca. |
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Authors:
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Parameswaran Ramachandran; Gareth A Palidwor; Christopher J Porter; Theodore J Perkins |
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Publication Detail:
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Type: JOURNAL ARTICLE Date: 2013-1-7 |
Journal Detail:
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Title: Bioinformatics (Oxford, England) Volume: - ISSN: 1367-4811 ISO Abbreviation: Bioinformatics Publication Date: 2013 Jan |
Date Detail:
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Created Date: 2013-1-9 Completed Date: - Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 9808944 Medline TA: Bioinformatics Country: - |
Other Details:
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Languages: ENG Pagination: - Citation Subset: - |
Affiliation:
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Ottawa Hospital Research Institute, Regenerative Medicine Program, K1H 8L6, Ottawa, Canada. |
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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