QAPA

QAPA quantifies alternative polyadenylation (APA) isoform abundance from conventional RNA-seq data to enable genome-wide analysis of APA-mediated post-transcriptional regulation.

Key Features:

• APA quantification from RNA-seq: Accurately quantifies APA isoform abundance using standard RNA-seq datasets.
• APA event inference: Infers alternative polyadenylation events genome-wide from conventional RNA-seq.
• Speed and sensitivity: Demonstrates improved computational speed and sensitivity relative to existing methods.
• Modeling for APA sequence code: Models RNA-seq data to reveal an APA sequence code linking sequence features to APA regulation.
• Detection of regulated APA programs: Identifies discrete, temporally coordinated APA programs exemplified during neurogenesis.
• Separation from alternative splicing: Enables analysis showing minimal overlap between genes regulated by alternative splicing and those regulated by APA.

Scientific Applications:

• Genome-wide APA profiling: Enables genome-wide characterization of alternative polyadenylation from conventional RNA-seq data.
• Neurogenesis APA programs: Detects temporally coordinated APA programs during neurogenesis.
• Regulatory mechanism delineation: Distinguishes APA-mediated regulation from alternative splicing by identifying minimal gene overlap.
• Sequence code discovery: Supports discovery and characterization of APA-associated sequence motifs through RNA-seq modeling.

Methodology:

Infers APA events from conventional RNA-seq data and models RNA-seq-derived isoform abundances to identify APA-associated sequence features.