Introduction

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.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.

Publications

  1. PVAAS: identify variants associated with aberrant splicing from RNA-seq.
    Cite this
    Wang L, Nie JJ, Kocher JP, 2015-05-01 - Bioinformatics (Oxford, England)

Credits

  1. Liguo Wang
    Developer

    Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, United States of America

  2. Jinfu J Nie
    Developer

    Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, United States of America

  3. Jean-Pierre A Kocher
    Investigator

    Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, United States of America

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Summary
AccessionBT007040
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByJean-Pierre A Kocher