Systematic evaluation of spliced alignment programs for RNA-seq data.
Systematic evaluation of spliced alignment programs for RNA-seq data.
复制标题
DOI：
10.1038/nmeth.2722
复制
发表时间：
2013-12
期刊：
影响因子：
48
通讯作者：
Bertone, Paul
中科院分区：
文献类型：
--
作者：
Engstrom, Par G.;Steijger, Tamara;Sipos, Botond;Grant, Gregory R.;Kahles, Andre;Raetsch, Gunnar;Goldman, Nick;Hubbard, Tim J.;Harrow, Jennifer;Guigo, Roderic;Bertone, Paul
作者比较了小鼠和人类数据集上的RNA-seq比对，使用基准，如比对产率，剪接点准确性和转录重建的适用性。这项工作突出了每个项目的优势，并讨论了RNA-seq分析中的突出需求。本文的在线版本（doi：10.1038/nmeth.2722）包含补充材料，可供授权用户使用。高通量RNA测序是一种越来越容易在全基因组范围内研究基因结构和活性的方法。RNA-seq数据分析的关键步骤是将部分转录物读数与参考基因组序列进行比对。为了评估当前映射软件的性能，我们邀请RNA-seq比对器的开发人员处理四个大型人类和小鼠RNA-seq数据集。总的来说，我们比较了26个映射协议的基础上11个程序和管道，并发现主要的性能差异的方法在众多的基准，包括对齐产量，碱基的准确性，错配和缺口的位置，外显子连接发现和适合的对齐转录重建。我们在真实的和模拟的RNA-seq数据上观察到一致的结果，证实了所采用的度量的相关性。RNA-seq比对方法的未来发展将受益于改进的多重映射读数的放置，现有基因注释的平衡利用以及减少剪接点的错误发现率。本文的在线版本（doi：10.1038/nmeth.2722）包含补充材料，可供授权用户使用。
Authors compare RNA-seq aligners on mouse and human data sets using benchmarks such as alignment yield, splice junction accuracy and suitability for transcript reconstruction. The work highlights the strength of each program and discusses outstanding needs in RNA-seq analysis. The online version of this article (doi:10.1038/nmeth.2722) contains supplementary material, which is available to authorized users. High-throughput RNA sequencing is an increasingly accessible method for studying gene structure and activity on a genome-wide scale. A critical step in RNA-seq data analysis is the alignment of partial transcript reads to a reference genome sequence. To assess the performance of current mapping software, we invited developers of RNA-seq aligners to process four large human and mouse RNA-seq data sets. In total, we compared 26 mapping protocols based on 11 programs and pipelines and found major performance differences between methods on numerous benchmarks, including alignment yield, basewise accuracy, mismatch and gap placement, exon junction discovery and suitability of alignments for transcript reconstruction. We observed concordant results on real and simulated RNA-seq data, confirming the relevance of the metrics employed. Future developments in RNA-seq alignment methods would benefit from improved placement of multimapped reads, balanced utilization of existing gene annotation and a reduced false discovery rate for splice junctions. The online version of this article (doi:10.1038/nmeth.2722) contains supplementary material, which is available to authorized users.
登录
查看更多内容
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
14.9
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
通讯作者：
Liu J
影响因子：
46.9
作者：
Trapnell C;Williams BA;Pertea G;Mortazavi A;Kwan G;van Baren MJ;Salzberg SL;Wold BJ;Pachter L
通讯作者：
Pachter L
影响因子：
12.3
作者：
Danecek P;Nellåker C;McIntyre RE;Buendia-Buendia JE;Bumpstead S;Ponting CP;Flint J;Durbin R;Keane TM;Adams DJ
通讯作者：
Adams DJ
影响因子：
48
作者：
Marbach, Daniel;Costello, James C.;Kueffner, Robert;Vega, Nicole M.;Prill, Robert J.;Camacho, Diogo M.;Allison, Kyle R.;Kellis, Manolis;Collins, James J.;Stolovitzky, Gustavo
通讯作者：
Stolovitzky, Gustavo