Scotty

Scotty estimates the sequencing read depth and sample size required to detect differential gene expression between two conditions in RNA-Seq experiments.

Key Features:

• Read depth estimation: Estimates the optimal number of sequencing reads required to detect differential gene expression between two conditions.
• Sample size recommendation: Recommends the number of samples needed to achieve user-defined goals and sufficient statistical power.
• Use of pilot and public data: Accepts preliminary pilot sample data or publicly available RNA-Seq datasets as input for analysis.
• Simulation of experimental scenarios: Simulates various experimental scenarios to evaluate detection power across different read depths and sample sizes.
• Tailored recommendations: Provides recommendations on sample size and read depth based on input data and user-defined objectives.

Scientific Applications:

• RNA-Seq experimental design: Planning sequencing depth and sample numbers for differential gene expression studies.
• Power analysis: Estimating the statistical power to detect expression differences under varying read depths and sample sizes.
• Pilot data evaluation: Assessing whether pilot or publicly available RNA-Seq datasets are sufficient to inform experimental design.

Methodology:

Analyzes input RNA-Seq pilot data or publicly available datasets and simulates experimental scenarios to evaluate detection power across varying read depths and sample sizes, then provides tailored recommendations.