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.
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
Contact – firstname.lastname@example.org