Detection of splice junctions from paired-end RNA-seq data by SpliceMap.
Detection of splice junctions from paired-end RNA-seq data by SpliceMap.
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DOI：
10.1093/nar/gkq211
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发表时间：
2010-08
影响因子：
14.9
通讯作者：
Wong WH
中科院分区：
文献类型：
--
作者：
Au KF;Jiang H;Lin L;Xing Y;Wong WH
选择性剪接是一种普遍存在的转录后过程，它不仅对细胞的正常功能起重要作用，而且与人类疾病有关。新开发的第二代测序技术提供了高通量数据（RNA-seq数据），以研究不同类型细胞中的可变剪接事件。在这里，我们提出了一种计算方法，剪接图，从RNA-seq数据检测剪接点。该方法不依赖于任何现有的基因结构注释，并且能够以高灵敏度和特异性发现新的剪接点。它可以处理长读段（50-100 nt），并可以利用配对读段信息来提高定位精度。输出中包含多个参数，以指示预测交汇点的可靠性，并帮助滤除错误预测。我们应用SpliceMap分析了来自人脑组织的2300万对50-nt读段。结果表明，在该测序深度下，RNA-seq可以支持可靠的剪接点检测，除了那些以非常低的水平存在的剪接点。与目前的方法相比，SpliceMap可以在不牺牲特异性的情况下实现12%的高灵敏度。
Alternative splicing is a prevalent post-transcriptional process, which is not only important to normal cellular function but is also involved in human diseases. The newly developed second generation sequencing technique provides high-throughput data (RNA-seq data) to study alternative splicing events in different types of cells. Here, we present a computational method, SpliceMap, to detect splice junctions from RNA-seq data. This method does not depend on any existing annotation of gene structures and is capable of finding novel splice junctions with high sensitivity and specificity. It can handle long reads (50–100 nt) and can exploit paired-read information to improve mapping accuracy. Several parameters are included in the output to indicate the reliability of the predicted junction and help filter out false predictions. We applied SpliceMap to analyze 23 million paired 50-nt reads from human brain tissue. The results show at this depth of sequencing, RNA-seq can support reliable detection of splice junctions except for those that are present at very low level. Compared to current methods, SpliceMap can achieve 12% higher sensitivity without sacrificing specificity.
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