scAPAtrap

scAPAtrap detects genome-wide alternative polyadenylation (APA) sites from 3' tag-based single-cell RNA sequencing (scRNA-seq) data to characterize APA dynamics and identify novel poly(A) sites.

Key Features:

• Whole-Genome Poly(A) Site Detection: Identifies poly(A) sites across the entire genome, enabling discovery of sites outside annotated genes.
• Precision and Sensitivity: Uses peak identification and poly(A) read anchoring to locate poly(A) sites with high precision, including sites with low read coverage.
• Annotation-Independent Analysis: Operates without relying on prior genome annotations, facilitating discovery of novel APA events.
• Comparative Performance: Demonstrated superior accuracy and sensitivity relative to scAPA and Sierra across multiple experimental technologies and species.

Scientific Applications:

• Exploration of APA Dynamics: Enables investigation of APA variation among cell types and within heterogeneous single-cell populations.
• Identification of Novel Poly(A) Sites: Detects previously unannotated poly(A) sites from 3' tag-based scRNA-seq data.
• Improvement of Genome Annotation: Contributes poly(A) site discoveries that can refine and expand existing genome annotations.

Methodology:

Processes 3' tag-based scRNA-seq data (e.g., CEL-seq and 10x Genomics) and applies peak identification and poly(A) read anchoring to localize poly(A) sites without using existing gene annotations.