Methods in enzymology | 2021
Quantifying alternative polyadenylation in RNAseq data with LABRAT.
Abstract
Alternative polyadenylation (APA) generates transcript isoforms that differ in their 3 UTR content and may therefore be subject to different regulatory fates. Although the existence of APA has been known for decades, quantification of APA isoforms from high-throughput RNA sequencing data has been difficult. To facilitate the study of APA in large datasets, we developed an APA quantification technique called LABRAT (Lightweight Alignment-Based Reckoning of Alternative Three-prime ends). LABRAT leverages modern transcriptome quantification approaches to determine the relative abundances of APA isoforms. In this manuscript we describe how LABRAT produces its calculations, provide a step-by-step protocol for its use, and demonstrate its ability to quantify APA in single-cell RNAseq data.