RNA序列
计算生物学
转录组
工作流程
计算机科学
管道(软件)
基因
核糖核酸
遗传学
生物
基因表达
数据库
程序设计语言
作者
Sayed Mohammad Ebrahim Sahraeian,Marghoob Mohiyuddin,Robert Sebra,Hagen Tilgner,Pegah Tootoonchi Afshar,Kin Fai Au,Narges Bani Asadi,Mark Gerstein,Wing Hung Wong,M Snyder,Eric E. Schadt,Hugo Y. K. Lam
标识
DOI:10.1038/s41467-017-00050-4
摘要
Abstract RNA-sequencing (RNA-seq) is an essential technique for transcriptome studies, hundreds of analysis tools have been developed since it was debuted. Although recent efforts have attempted to assess the latest available tools, they have not evaluated the analysis workflows comprehensively to unleash the power within RNA-seq. Here we conduct an extensive study analysing a broad spectrum of RNA-seq workflows. Surpassing the expression analysis scope, our work also includes assessment of RNA variant-calling, RNA editing and RNA fusion detection techniques. Specifically, we examine both short- and long-read RNA-seq technologies, 39 analysis tools resulting in ~120 combinations, and ~490 analyses involving 15 samples with a variety of germline, cancer and stem cell data sets. We report the performance and propose a comprehensive RNA-seq analysis protocol, named RNACocktail, along with a computational pipeline achieving high accuracy. Validation on different samples reveals that our proposed protocol could help researchers extract more biologically relevant predictions by broad analysis of the transcriptome.
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