MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.
MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.
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DOI：
10.1093/nar/gkq622
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发表时间：
2010-10
影响因子：
14.9
通讯作者：
Liu J
中科院分区：
文献类型：
--
作者：
Wang K;Singh D;Zeng Z;Coleman SJ;Huang Y;Savich GL;He X;Mieczkowski P;Grimm SA;Perou CM;MacLeod JN;Chiang DY;Prins JF;Liu J
跨越剪接点的读数的准确映射是所有使用RNA-seq数据的分析技术的关键组成部分。我们介绍了第二代剪接检测算法，MapSplice，其重点是高灵敏度和特异性的剪接检测以及CPU和内存的效率。MapSplice可应用于短（<75 bp）和长（≥75 bp）读段。MapSplice不依赖于剪接位点特征或内含子长度，因此它可以检测新的规范以及非规范剪接。MapSplice利用给定剪接的读段比对的质量和多样性来提高准确性。我们证明了MapSplice在一组模拟RNA-seq数据上比TopHat和SpliceMap具有更高的灵敏度和特异性。实验研究也支持了算法的准确性。来自八个乳腺癌RNA-seq数据集的剪接接头概括了全球水平上选择性剪接的广泛性以及乳腺癌分子亚型之间的差异。这些组合结果表明，MapSplice是一种高度准确的算法，用于将RNA-seq读数与剪接点进行比对。软件下载网址：http://www.netlab.uky.edu/p/bioinfo/MapSplice。
The accurate mapping of reads that span splice junctions is a critical component of all analytic techniques that work with RNA-seq data. We introduce a second generation splice detection algorithm, MapSplice, whose focus is high sensitivity and specificity in the detection of splices as well as CPU and memory efficiency. MapSplice can be applied to both short (<75 bp) and long reads (≥75 bp). MapSplice is not dependent on splice site features or intron length, consequently it can detect novel canonical as well as non-canonical splices. MapSplice leverages the quality and diversity of read alignments of a given splice to increase accuracy. We demonstrate that MapSplice achieves higher sensitivity and specificity than TopHat and SpliceMap on a set of simulated RNA-seq data. Experimental studies also support the accuracy of the algorithm. Splice junctions derived from eight breast cancer RNA-seq datasets recapitulated the extensiveness of alternative splicing on a global level as well as the differences between molecular subtypes of breast cancer. These combined results indicate that MapSplice is a highly accurate algorithm for the alignment of RNA-seq reads to splice junctions. Software download URL: http://www.netlab.uky.edu/p/bioinfo/MapSplice.
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影响因子：
12.3
作者：
Kircher M;Stenzel U;Kelso J
通讯作者：
Kelso J
影响因子：
14.9
作者：
Richard H;Schulz MH;Sultan M;Nürnberger A;Schrinner S;Balzereit D;Dagand E;Rasche A;Lehrach H;Vingron M;Haas SA;Yaspo ML
通讯作者：
Yaspo ML
影响因子：
4.4
作者：
Koscielny, Gautier;Le Texier, Vincent;Gautheret, Daniel
通讯作者：
Gautheret, Daniel
影响因子：
8
作者：
Pollock, P. M.;Gartside, M. G.;Dejeza, L. C.;Powell, M. A.;Mallon, M. A.;Davies, H.;Mohammadi, M.;Futreal, P. A.;Stratton, M. R.;Trent, J. M.;Goodfellow, P. J.
通讯作者：
Goodfellow, P. J.
影响因子：
7
作者：
Li, Heng;Ruan, Jue;Durbin, Richard
通讯作者：
Durbin, Richard