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

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

Author information

1
Department of Biology, Boston College, Chestnut Hill, MA 02467, USA.

Abstract

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 http://euler.bc.edu/marthlab/scotty/scotty.php

PMID:
23314327
PMCID:
PMC3582267
DOI:
10.1093/bioinformatics/btt015
[Indexed for MEDLINE]
Free PMC Article
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