Introduction

Accurate identification of genetic variants such as single-nucleotide polymorphisms (SNPs) or RNA editing sites from RNA-Seq reads is important, yet challenging, because it necessitates a very low false-positive rate in read mapping. Although many read aligners are available, no single aligner was specifically developed or tested as an effective tool for SNP and RNA editing prediction.We present RASER, an accurate read aligner with novel mapping schemes and index tree structure that aims to reduce false-positive mappings due to existence of highly similar regions. We demonstrate that RASER shows the best mapping accuracy compared with other popular algorithms and highest sensitivity in identifying multiply mapped reads. As a result, RASER displays superb efficacy in unbiased mapping of the alternative alleles of SNPs and in identification of RNA editing sites.RASER is written in C++ and freely available for download at https://github.com/jaegyoonahn/RASER.

Publications

  1. RASER: reads aligner for SNPs and editing sites of RNA.
    Cite this
    Ahn J, Xiao X, 2015-12-01 - Bioinformatics (Oxford, England)
  2. Accurate identification of A-to-I RNA editing in human by transcriptome sequencing.
    Cite this
    Bahn JH, Lee JH, Li G, Greer C, Peng G, Xiao X, 2012-01-01 - Genome research

Credits

  1. Jaegyoon Ahn
    Developer

    Department of Integrative Biology and Physiology and the Molecular Biology Institute, University of California Los Angeles, United States of America

  2. Xinshu Xiao
    Investigator

    Department of Integrative Biology and Physiology and the Molecular Biology Institute, University of California Los Angeles, United States of America

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Summary
AccessionBT001741
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByXinshu Xiao