DPAC: A tool for differential poly(A)-cluster usage from poly(A)-targeted RNAseq data

Research output: Contribution to journalArticle

Abstract

Poly(A)-tail targeted RNAseq approaches, such as 39READS, PAS-Seq and Poly(A)-ClickSeq, are becoming popular alternatives to random-primed RNAseq to focus sequencing reads just to the 39 ends of polyadenylated RNAs to identify poly(A)-sites and characterize changes in their usage. Additionally, we and others have demonstrated that these approaches perform similarly to other RNAseq strategies for differential gene expression analysis, while saving on the volume of sequencing data required and providing a simpler library synthesis strategy. Here, we present DPAC (Differential Poly(A)-Clustering); a streamlined pipeline for the preprocessing of poly(A)-tail targeted RNAseq data, mapping of poly(A)-sites, poly(A)-site clustering and annotation, and determination of differential poly(A)-cluster usage using DESeq2. Changes in poly(A)-cluster usage is simultaneously used to report differential gene expression, differential terminal exon usage and alternative polyadenylation (APA).

Original languageEnglish (US)
Pages (from-to)1825-1830
Number of pages6
JournalG3: Genes, Genomes, Genetics
Volume9
Issue number6
DOIs
StatePublished - Jan 1 2019

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Keywords

  • Alternative
  • ClickSeq
  • Differential
  • Expression
  • Gene
  • Poly(A)-sites
  • Polyadenylation

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

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