Improving RNA-Seq Precision with MapAl.
Improving RNA-Seq Precision with MapAl.
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DOI：
10.3389/fgene.2012.00028
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发表时间：
2012
影响因子：
3.7
通讯作者：
Kreil DP
中科院分区：
文献类型：
--
作者：
Labaj PP;Linggi BE;Wiley HS;Kreil DP
在目前可用的RNA-Seq管道中，大多数基因的表达估计都非常嘈杂。我们在这里介绍MapAl，一个RNA-Seq表达分析工具，建立在既定的程序Bowtie和Cufflinks。在RNA-Seq reads的后处理中，它结合了已经处于reads比对阶段的基因模型，将可靠测量的已知转录本数量增加了50%。与其他可用的管道相比，添加从头鉴定的基因可以可靠地评估转录本总数的两倍。这种实质性的改进具有普遍的相关性：测量精度决定了任何分析可靠地识别重要信号的能力，例如在差异表达的筛选中，与实验设计是否包含重复无关。
With currently available RNA-Seq pipelines, expression estimates for most genes are very noisy. We here introduce MapAl, a tool for RNA-Seq expression profiling that builds on the established programs Bowtie and Cufflinks. In the post-processing of RNA-Seq reads, it incorporates gene models already at the stage of read alignment, increasing the number of reliably measured known transcripts consistently by 50%. Adding genes identified de novo then allows a reliable assessment of double the total number of transcripts compared to other available pipelines. This substantial improvement is of general relevance: Measurement precision determines the power of any analysis to reliably identify significant signals, such as in screens for differential expression, independent of whether the experimental design incorporates replicates or not.