JunctionSeq

JunctionSeq detects differential exon and splice-junction usage from RNA-Seq data to identify alternative isoform regulation, including detection of novel splice junctions when transcript annotations are incomplete.

Key Features:

• Detection of Differential Usage: Detects differential usage of exonic regions and splice junctions from RNA-Seq data without requiring an isoform assembly step.
• Novel Splice-Junction Detection: Identifies novel splice junctions and enables analysis when transcript annotations are incomplete.
• Statistical Framework: Extends the DEXSeq statistical methodologies to test differential usage at both exon and splice-junction levels.
• Visualization: Generates visual summaries of differential exon and splice-junction usage to aid result interpretation.

Scientific Applications:

• Alternative Splicing Analysis: Detection and characterization of alternative isoform regulation and alternative splicing events from RNA-Seq data.
• Isoform-Level Expression Studies: Precise isoform-level differential usage analysis for studies of gene regulation.
• Organism-Specific Studies: Applied to rat pineal gland and Toxoplasma gondii data, detecting known and previously validated AIR genes with perfect gene-level hypothesis test results (19/19).

Methodology:

Extends DEXSeq-like statistical techniques to model and test differential usage of exonic regions and splice junctions, incorporating novel splice junctions and operating without an isoform assembly step.