Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression

Bioinformatics. 2013 Mar 1;29(5):656-7. doi: 10.1093/bioinformatics/btt015. Epub 2013 Jan 12.


Motivation: 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?

Results: Scotty is 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

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Gene Expression
  • Gene Expression Profiling / methods*
  • Humans
  • Internet
  • Sequence Analysis, RNA / methods*
  • Software*