PolyAseqTrap: a universal tool for genome-wide identification and quantification of polyadenylation sites from different 3′ end sequencing data

Alternative polyadenylation (APA) is a pervasive RNA-processing mechanism in eukaryotes that significantly promotes transcriptome and proteome diversity. Here we proposed PolyAseqTrap, an R package for probing polyA sites from diverse 3' sequencing data. PolyAseqTrap implements a polyA read prioritization strategy to determine precise positions of polyA sites. Particularly, it incorporates a transferrable cross-species deep learning model for mitigating the long-pending internal priming problem. Moreover, PolyAseqTrap employs a weighted density peak clustering method to reducing microheterogeneity impact in different species. We evaluated PolyAseqTrap using data from 16 different 3' sequencing techniques across multiple species, demonstrating the effectiveness and robustness of PolyAseqTrap.