Unleash the power within RNA-seq

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 researchers at Roche Sequencing Solutions 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, they 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. The researchers 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 their 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.

The RNACocktail analysis protocol

rna-seq

RNACocktail is a comprehensive protocol of RNA-seq data analysis. The figure summarizes the widely used approaches for the key steps over the broad spectrum of RNA-seq analysis and also succinctly captures the possible workflows one can use to analyse RNA-seq data

Availability – The computational pipeline is open-sourced and available at http://bioinform.github.io/rnacocktail/.

Sahraeian SME, Mohiyuddin M, Sebra R, Tilgner H, Afshar PT, Au KF, Bani Asadi N, Gerstein MB, Wong WH, Snyder MP, Schadt E, Lam HYK. (2017) Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis. Nat Commun 8(1):59. [article]

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