IPSA

IPSA quantifies and analyzes RNA splicing from RNA-seq data by extracting splice-junction and splice-site counts, computing exon- and intron-centric splicing indices with separate 5' and 3' measures, and characterizing micro-exons and local splice-graph structures.

Key Features:

• Quantification of splice junctions and boundaries: Quantifies splice junctions and splice-site boundaries from RNA-seq alignments to produce junction-centered and boundary-centered counts.
• Calculation of splicing indices: Computes exon-centric and intron-centric splicing indices and decomposes splicing completeness into separate 5' and 3' measures.
• Analysis of micro-exons and splice-graph structure: Analyzes micro-exons and local splice-graph structures to characterize complex splicing events.
• BAM-file-processing pipeline (bam2ssj): Implements a BAM-file-processing pipeline, bam2ssj, that processes strand-specific reads aligning to splice junctions or overlapping splice sites.

Scientific Applications:

• Alternative splicing: Quantitative analysis of alternative splicing events from RNA-seq data.
• Gene regulation: Assessment of how splicing variation affects gene regulation.
• Transcriptome diversity: Characterization of transcriptome diversity arising from alternative splice forms.
• Splicing in health and disease: Investigation of functional implications of splicing variations in health and disease contexts.

Methodology:

Adopts an intron-centric perspective that decomposes splicing completeness into separate 5' and 3' measures and uses the bam2ssj BAM-file-processing pipeline to process strand-specific reads that align to splice junctions or overlap splice sites.