SplicingTypesAnno

SplicingTypesAnno annotates intron retention, exon skipping, alternative donor site (5' splice sites), and alternative acceptor site (3' splice sites) from RNA-Seq alignment files to provide exon- and intron-level annotations for analysis of alternative splicing.

Key Features:

• Annotated splicing types: Identifies intron retention, exon skipping, alternative donor site (5' splice sites), and alternative acceptor site (3' splice sites) from RNA-Seq data.
• Exon/intron-level resolution: Provides detailed annotations at the exon or intron level.
• Annotation comparison: Compares extracted events against existing annotations from GTF/GFF files to identify novel alternative splicing sites.
• Two-level analysis capability: Supports genome-scale annotation for high-performance computing and gene-scale annotation for analysis of individual genes or small datasets.
• IGV-compatible outputs: Generates BED files compatible with the Integrative Genomics Viewer (IGV) for genomic visualization.
• Implementation: Implemented as an R package that operates as a post-processing utility for RNA-Seq alignment files.

Scientific Applications:

• Alternative splicing research: Enables identification and characterization of intron retention, exon skipping, and alternative splice site usage to study splicing regulation.
• Novel splice site discovery: Supports detection of previously unannotated alternative donor and acceptor sites through comparison with GTF/GFF annotations.
• Visualization and validation: Produces BED files for IGV to facilitate visualization and inspection of annotated splicing events within genomic context.

Methodology:

Processes RNA-Seq alignment files to extract alternative splicing events, annotates events at the exon/intron level, compares them with GTF/GFF annotations to identify novel splicing variations, and outputs BED files for IGV; implemented as an R package operating as a post-processing utility for sequence alignment files.