A common question arises at the beginning of every experiment where RNA-Seq is used to detect differential gene expression between two conditions: How many reads should we sequence?
Now, researchers at Boston College have developed Scotty, an interactive web-based application that assists biologists to design an experiment with an appropriate sample size and read depth to satisfy the user-defined experimental objectives. This design can be based on data available from either pilot samples or publicly available datasets.
AVAILABILITY: Scotty can be freely accessed on the web at http://euler.bc.edu/marthlab/scotty/scotty.php
- Busby MA, Stewart C, Miller C, Grzeda K, Marth G. (2012) Scotty: A Web Tool For Designing RNA-Seq Experiments to Measure Differential Gene Expression. Bioinformatics [Epub ahead of print]. [abstract]