VaSP

VaSP quantifies and discovers genome-wide variable alternative splicing events from short-read RNA-seq data to prioritize causal pre-mRNA splicing events in genome-wide association studies.

Key Features:

• Quantification of splicing variants: VaSP quantifies splicing variants from short-read RNA-seq datasets.
• Genotype-specific splicing discovery: VaSP discovers genotype-specific splicing (GSS) events for population-level analysis.
• Visualization of gene splicing information: VaSP generates publication-quality multi-panel figures for gene splicing information in a population (note: this function was removed due to deprecation of the dependent package Sushi).

Scientific Applications:

• Alternative splicing analysis in plants: VaSP enables versatile alternative splicing analysis in plant species.
• Genome-wide association studies: GSS events discovered by VaSP can be used as markers for GWAS to prioritize candidate causal pre-mRNA splicing events and corresponding genomic variations.
• Stress response studies: VaSP can identify genotype-specific splicing events associated with stress responses, such as salt stress in rice.

Methodology:

VaSP analyzes short-read RNA-seq datasets to quantify splicing variants and discover genotype-specific splicing events; these GSS events are then used as markers in GWAS to identify associations with phenotypic traits.