Mapping RNA-seq Reads with STAR.
Mapping RNA-seq Reads with STAR.
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DOI：
10.1002/0471250953.bi1114s51
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发表时间：
2015-09-03
影响因子：
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通讯作者：
Gingeras TR
中科院分区：
文献类型：
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作者：
Dobin A;Gingeras TR
将大量高通量测序读数映射到参考基因组是RNA-seq数据分析的基础步骤之一。星星软件包以高精度和高速度执行此任务。除了检测注释的和新的剪接点，星星能够发现更复杂的RNA序列排列，如嵌合和环状RNA。星星可以比对任何长度的剪接序列，具有中等错误率，为新兴的测序技术提供可扩展性。星星生成可用于许多下游分析的输出文件，例如转录物/基因表达定量、差异基因表达、新亚型重建、信号可视化等。在本单元中，我们描述了产生各种输出文件的计算协议，使用不同的RNA-seq数据库，并利用不同的映射策略。星星是开源软件，可以在Unix、Linux或Mac OS X系统上运行。
Mapping of large sets of high-throughput sequencing reads to a reference genome is one of the foundational steps in RNA-seq data analysis. The STAR software package performs this task with high levels of accuracy and speed. In addition to detecting annotated and novel splice junctions, STAR is capable of discovering more complex RNA sequence arrangements, such as chimeric and circular RNA. STAR can align spliced sequences of any length with moderate error rates providing scalability for emerging sequencing technologies. STAR generates output files that can be used for many downstream analyses such as transcript/gene expression quantification, differential gene expression, novel isoform reconstruction, signal visualization, and so forth. In this unit we describe computational protocols that produce various output files, use different RNA-seq datatypes, and utilize different mapping strategies. STAR is Open Source software that can be run on Unix, Linux or Mac OS X systems.