Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis

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 th...

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Vydáno v:Nature communications Ročník 8; číslo 1; s. 59 - 15
Hlavní autoři: Sahraeian, Sayed Mohammad Ebrahim, Mohiyuddin, Marghoob, Sebra, Robert, Tilgner, Hagen, Afshar, Pegah T., Au, Kin Fai, Bani Asadi, Narges, Gerstein, Mark B., Wong, Wing Hung, Snyder, Michael P., Schadt, Eric, Lam, Hugo Y. K.
Médium: Journal Article
Jazyk:angličtina
Vydáno: London Nature Publishing Group UK 05.07.2017
Nature Portfolio
Témata:
631/114/2785
631/61/514
Base Sequence
Cell Line
Embryonic Stem Cells
Humanities and Social Sciences
Humans
multidisciplinary
Science
Science (multidisciplinary)
Transcriptome
ISSN:2041-1723, 2041-1723
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Shrnutí: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. RNA-seq is widely used for transcriptome analysis. Here, the authors analyse a wide spectrum of RNA-seq workflows and present a comprehensive analysis protocol named RNACocktail as well as a computational pipeline leveraging the widely used tools for accurate RNA-seq analysis.
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ISSN:2041-1723
2041-1723
DOI:10.1038/s41467-017-00050-4