PeakATail: precision-first poly(A)-site calling and calibrated alternative polyadenylation analysis in single-cell RNA-seq

Abstract

Most human genes can end their messenger RNAs at more than one position, and the choice shifts between cell types. Single-cell sequencing reads that choice in individual cells, but two questions are seldom asked: are the reported sites real, and does the test for a cell-type difference hold its error rate? Here we introduce our tool PeakATail, which calls polyadenylation sites from reads still carrying a piece of the tail, ranks them by how many distinct molecules carry that evidence, discards sites where adenosine-rich genomic sequence mimics a tail, and pairs them with a differential test whose error rate is measured, not assumed. The evidence is scarce, so the tool is built to be right rather than complete. Across four libraries from two species, 71 to 83 percent of its calls fall within 100 bases of a curated atlas, over thirty times the shuffled-control rate; long reads from different donors support 76.5 percent of the human calls. The cost is sensitivity. Only one of six test configurations held its false-positive rate under shuffled labels; with it, 15,942 cell-type switches replicated across twelve lung cancer patients and none in ten shuffled-label runs. One pre-registered target was missed and is reported.