Designing alternative splicing RNA-seq studies

D esigning an RNA-seq study depends critically on its specific goals, technology and underlying biology, which renders general guidelines inadequate.  A team led by researchers at IRB Barcelona have developed a Bayesian framework to customize experiments so that goals can be attained and resources are not wasted, with a focus on alternative splicing.

The research team studied how read length, sequencing depth, library preparation and the number of replicates affects cost-effectiveness of single-sample and group comparison studies. Optimal settings varied strongly according to the target organism or tissue (potential 50%-500% cost cuts) and, interestingly, short reads outperformed long reads for standard analyses. Their framework learns key characteristics for study design from the data, and predicts if and how to continue experimentation. These predictions matched several follow-up experimental data sets that were used for validation.

rna-seq

Representing uncertainty via simulation

Availability – casper package at www.bioconductor.org/packages/release/bioc/html/casper.html, Supplementary Manual by typing casperDesign() at the R prompt. Supplementary statistical methods, model assessment and results at Bioinformatics online

Contactrosselldavid@gmail.com

Stephan-Otto Attolini C, Peña V, Rossell D. (2015) Designing alternative splicing RNA-seq studies. Beyond generic guidelines. Bioinformatics [Epub ahead of print]. [abstract]

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