Designing alternative splicing RNA-seq studies. Beyond generic guidelines.

ABSTRACT:

Motivation

Designing an RNA-seq study depends critically on its specific goals, technology and underlying biology, which renders general guidelines inadequate. We propose a Bayesian framework to customize experiments so that goals can be attained and resources are not wasted, with a focus on alternative splicing.

Results

We 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. Our framework learns key characteristics for study design from the data, and predicts if and how to continue

SUBMITTER: Stephan-Otto Attolini C 

PROVIDER: S-EPMC4757954 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature