MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data
MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data
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DOI：
10.1093/bioinformatics/btt001
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发表时间：
2013-02-15
期刊：
影响因子：
5.8
通讯作者：
Perkins, Theodore J.
中科院分区：
文献类型：
--
作者：
Ramachandran, Parameswaran;Palidwor, Gareth A.;Perkins, Theodore J.
结果：在本文中，我们研究了使用链互相关来估计单端数据的平均片段长度，并表明传统的估计方法具有混合可靠性。我们观察到基因组不同部分的可映射性可能会在互相关计算中引入人为偏差，导致片段长度估计不正确。我们提出了一种称为可映射性敏感互相关（MaSC）的新方法，它消除了这种偏差并允许准确可靠的片段长度估计。我们分析了这种方法的计算复杂性，并在 NGS 数据集测试套件上评估其性能，证明其相对于传统互相关分析的优越性。 可用性：我们方法的开源 Perl 实现可在 ext-link-type="uri" xlink:href="http://www.perkinslab.ca/Software.html" 上获得。 xmlns:xlink="http://www.w3.org/1999/xlink">http://www.perkinslab.ca/Software.html。联系方式：tperkins@ohri.ca补充信息：ext-link-type="uri" xlink:href="http://bioinformatics.oxfordjournals.org/cgi/content/full/btt001/DC1" xmlns:xlink="http://www.w3.org/1999/xlink">补充数据可在生物信息学在线获取。
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.Availability: An open-source Perl implementation of our approach is available at ext-link-type="uri" xlink:href="http://www.perkinslab.ca/Software.html" xmlns:xlink="http://www.w3.org/1999/xlink">http://www.perkinslab.ca/Software.html.Contact: tperkins@ohri.caSupplementary information: ext-link-type="uri" xlink:href="http://bioinformatics.oxfordjournals.org/cgi/content/full/btt001/DC1" xmlns:xlink="http://www.w3.org/1999/xlink">Supplementary data are available at Bioinformatics online.