tools-only Differential Splicing - Usage Guide
Overview
Detect differential alternative splicing between experimental conditions. Identifies splicing events that change significantly between groups, reporting both statistical significance and effect size (delta PSI).
Prerequisites
# rMATS-turbo
pip install rmats-turbo
# SUPPA2
pip install suppa
# leafcutter (R)
# install.packages('devtools')
# devtools::install_github('davidaknowles/leafcutter/leafcutter')
# Python dependencies
pip install pandas numpy scipy
Quick Start
Tell your AI agent what you want to do:
- "Find differential splicing between tumor and normal samples"
- "Compare splicing patterns between treatment and control groups"
- "Identify genes with significant splicing changes"
- "Run differential splicing analysis on my RNA-seq data"
Example Prompts
rMATS Analysis
"I have BAM files from control and treatment conditions. Run rMATS-turbo to find differential splicing events."
"Compare exon skipping between my two sample groups using rMATS."
SUPPA2 Analysis
"Use SUPPA2 diffSplice to compare splicing between conditions from my TPM data."
"Find differential splicing events with delta PSI greater than 0.2."
leafcutter Analysis
"Run leafcutter differential splicing analysis to find novel differential intron usage."
"Identify differential splicing at intron clusters between my conditions."
What the Agent Will Do
- Organize samples by condition/group
- Run differential splicing analysis with selected tool
- Calculate FDR-corrected p-values and delta PSI
- Filter significant events (default: FDR < 0.05, |deltaPSI| > 0.1)
- Generate ranked list of differential events by significance and effect size
Tips
- Use |deltaPSI| > 0.1 for discovery, > 0.2 for high-confidence sets
- rMATS-turbo combines quantification and differential testing in one run
- SUPPA2 tends to be more stringent, returning fewer significant events
- leafcutter is good for novel junction discovery without annotation bias
- Always check junction read support for significant events
Related Skills
- splicing-quantification - Calculate PSI values first
- isoform-switching - Analyze functional consequences
- sashimi-plots - Visualize significant events
- read-alignment/star-alignment - STAR 2-pass alignment required