PVAAS: Identify variants associated with aberrant splicing from RNA-seq

Research output: Contribution to journalArticle

1 Scopus citations

Abstract

Motivation: RNA-seq has been widely used to study the transcriptome. Comparing to microarray, sequencing-based RNA-seq is able to identify splicing variants and single nucleotide variants in one experiment simultaneously. This provides unique opportunity to detect variants that associated with aberrant splicing. Despite the popularity of RNA-seq, no bioinformatics tool has been developed to leverage this advantage to identify variants associated with aberrant splicing. Results: We have developed PVAAS, a tool to identify single nucleotide variants that associated with aberrant alternative splicing from RNA-seq data. PVAAS works in three steps: (i) identify aberrant splicings; (ii) use user-provided variants or perform variant calling; (iii) assess the significance of association between variants and aberrant splicing events.

Original languageEnglish (US)
Pages (from-to)1668-1670
Number of pages3
JournalBioinformatics
Volume31
Issue number10
DOIs
StatePublished - 2015

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Fingerprint Dive into the research topics of 'PVAAS: Identify variants associated with aberrant splicing from RNA-seq'. Together they form a unique fingerprint.

  • Cite this