MAAPER: model-based analysis of alternative polyadenylation using 3' end-linked reads

Genome Biol. 2021 Aug 10;22(1):222. doi: 10.1186/s13059-021-02429-5.


Most eukaryotic genes express alternative polyadenylation (APA) isoforms. A growing number of RNA sequencing methods, especially those used for single-cell transcriptome analysis, generate reads close to the polyadenylation site (PAS), termed nearSite reads, hence inherently containing information about APA isoform abundance. Here, we present a probabilistic model-based method named MAAPER to utilize nearSite reads for APA analysis. MAAPER predicts PASs with high accuracy and sensitivity and examines different types of APA events with robust statistics. We show MAAPER's performance with both bulk and single-cell data and its applicability in unpaired or paired experimental designs.

Keywords: 3′ end reads; Alternative polyadenylation; Bioinformatic tool; Cellular stress; RNA sequencing; Trophoblasts.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3' Untranslated Regions*
  • Animals
  • Computational Biology
  • Gene Expression*
  • Humans
  • Mice
  • Models, Theoretical
  • NIH 3T3 Cells
  • Polyadenylation*
  • Sequence Analysis, RNA
  • Single-Cell Analysis
  • Transcriptome


  • 3' Untranslated Regions