scTail: precise polyadenylation site detection and its alternative usage analysis from reads 1 preserved 3′ scRNA-seq data

The first-strand reads (often reads 1) of three-prime single-cell RNA-seq (3' scRNA-seq) can contain informative cDNA for analysis of polyadenylation sites (PAS), but are often overlooked or trimmed. Here, we describe a computational method, scTail, to identify PAS using first-strand reads and quantify its expression leveraging second-strand reads, consequently enabling detection of alternative PAS usage. Compared with other methods, scTail detects PAS more precisely and retains high sensitivity. Furthermore, we demonstrated that combining scTail and BRIE2 can discover differential alternative PAS usage in various biological processes including cancers and time-series development, giving critical insight into PAS regulation.