SUPPA

SUPPA quantifies alternative splicing by computing Percentage Spliced In (PSI) values from RNA sequencing transcript quantifications to enable comparative analysis of splicing events.

Key Features:

• Fast Quantification: Calculates Percentage Spliced In (PSI) values using fast transcript quantification methods from RNA-seq data.
• Accuracy and Speed: Achieves accuracy comparable or superior to standard methods on simulated and real RNA-seq data while providing over 1000-fold speed improvements versus traditional approaches.
• Annotation Sensitivity: Performance depends on annotation choice, with better splicing estimates obtained using complete transcript annotations rather than increasing transcript counts per gene.
• De novo Reconstruction Compatibility: Can be coupled with de novo transcript reconstruction methods, although this coupling does not yield higher accuracies than known-transcript quantification.
• Implementation: Implemented in Python 2.7.

Scientific Applications:

• Splicing Analysis: Enables systematic, large-scale analysis of alternative splicing events across conditions using PSI metrics derived from RNA-seq.
• Disease Research: Supports investigation of alternative splicing alterations relevant to diseases, particularly cancer.

Methodology:

SUPPA calculates relative inclusion values of alternative splicing events by exploiting fast transcript quantification; coupling with de novo transcript reconstruction methods has been shown not to improve accuracy over known-transcript quantification while remaining comparable to existing methodologies.