More than half of human genes undergo alternative polyadenylation (APA) and generate mRNA transcripts with varying lengths. Increasing awareness of APA’s role in human health and disease has propelled the development of several 3’ sequencing (3’Seq) techniques. Despite the recent data explosion, computational tools that are precisely designed for 3’Seq data are not well established. PolyA-miner is developed specifically for 3’Seq data, it accounts for all non‐proximal to non‐distal APA switches using vector projections and reflect precise gene level 3’UTR changes. PolyA-miner is less susceptible to inherent data variations can also to effectively identify novel APA sites that are otherwise undetected using reference-based approaches. With the emerging importance of alternative polyadenylation in studying human diseases, PolyA-miner can significantly accelerate data analysis and help decoding the missing pieces of underlying alternative polyadenylation dynamics.