CADBURE: A generic tool to evaluate the performance of spliced aligners on RNA-Seq data.
CADBURE: A generic tool to evaluate the performance of spliced aligners on RNA-Seq data.
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DOI：
10.1038/srep13443
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发表时间：
2015-08-25
影响因子：
4.6
通讯作者：
Liang C
中科院分区：
文献类型：
--
作者：
Kumar PK;Hoang TV;Robinson ML;Tsonis PA;Liang C
在基于RNA-Seq的转录组分析中，最基本的任务是将数百万个短片段与参考基因组或转录组进行比对。从许多现有的RNA-Seq比对程序包中为手头的数据集选择合适的工具仍然是下游分析的关键挑战。为了方便这一选择，我们设计了一个新的工具，用于基于唯一对齐读取的相对可靠性(CADBURE)来比较用户数据的对齐结果。CADBURE可以使用相同的比对器轻松评估不同的比对器或不同的参数集，并为任何RNA-Seq数据集选择最佳的比对结果。CADBURE的优势包括能够比较比对结果，而不需要合成数据，如模拟基因组、比对再生和随机二次抽样数据集。差异表达基因(DEG)分析支持CADBURE选择比对结果的益处。我们证明，使用CADBURE从许多不同的比对结果中选择最佳比对可以改变DEG的数量，最高可达10%。特别是，CADBURE选择的比对结果在DEG分析中有利于较少的假阳性。我们还通过RT-qPCR验证实验验证了18个基因的差异表达。CADBURE是一个开源工具(http://cadbure.sourceforge.net/).
The fundamental task in RNA-Seq-based transcriptome analysis is alignment of millions of short reads to the reference genome or transcriptome. Choosing the right tool for the dataset in hand from many existent RNA-Seq alignment packages remains a critical challenge for downstream analysis. To facilitate this choice, we designed a novel tool for comparing alignment results of user data based on the relative reliability of uniquely aligned reads (CADBURE). CADBURE can easily evaluate different aligners, or different parameter sets using the same aligner, and selects the best alignment result for any RNA-Seq dataset. Strengths of CADBURE include the ability to compare alignment results without the need for synthetic data such as simulated genomes, alignment regeneration and randomly subsampled datasets. The benefit of a CADBURE selected alignment result was supported by differentially expressed gene (DEG) analysis. We demonstrated that the use of CADBURE to select the best alignment from a number of different alignment results could change the number of DEGs by as much as 10%. In particular, the CADBURE selected alignment result favors fewer false positives in the DEG analysis. We also verified differential expression of eighteen genes with RT-qPCR validation experiments. CADBURE is an open source tool (http://cadbure.sourceforge.net/).