ISVASE

ISVASE identifies sequence variants associated with splicing events from RNA-seq data to detect variants that influence RNA splicing.

Key Features:

• Detection of Sequence Variants (SVASE): Identifies sequence variants associated with splicing events by analyzing RNA-seq data.
• Split-read-based identification: Uses only split-reads for variant identification at splice junctions.
• Junction-part-specific calling: Independently identifies sequence variants in each part of a splicing junction.
• Multi-pass rule-dependent and statistical filtering: Employs multi-pass stringent rule-dependent filters combined with statistical filters.
• Splicing signal evaluation: Evaluates splicing signals to support accurate variant-splicing associations.
• Exon-exon junction shift detection: Detects additional exon-exon junction shift events when known splicing events are provided.
• Integration of prior variant data: Supports incorporation of known DNA mutation and/or RNA editing data.
• Precision and performance: Reports higher precision and consistency with a short running time.

Scientific Applications:

• SVASE discovery: Identify sequence variants associated with splicing events from RNA-seq datasets.
• Impact assessment of DNA mutations and RNA editing: Assess how DNA mutations and/or RNA editing affect RNA splicing.
• Novel splicing event detection: Detect novel splicing events and exon-exon junction shifts.
• Splicing regulatory element studies: Support analyses of splicing regulatory elements linked to variant-induced splicing changes.
• Functional analysis of variants: Provide variant calls for downstream functional analyses of sequence variants affecting splicing.

Methodology:

Analyzes RNA-seq split-reads, applies multi-pass stringent rule-dependent filters and statistical filters, independently calls variants in each splice-junction part, and evaluates splicing signals.