Introduction

The accurate mapping of reads that span splice junctions is a critical component of all analytic techniques that work with RNA-seq data. We introduce a second generation splice detection algorithm, MapSplice, whose focus is high sensitivity and specificity in the detection of splices as well as CPU and memory efficiency. MapSplice can be applied to both short (<75 bp) and long reads (≥ 75 bp). MapSplice is not dependent on splice site features or intron length, consequently it can detect novel canonical as well as non-canonical splices. MapSplice leverages the quality and diversity of read alignments of a given splice to increase accuracy. We demonstrate that MapSplice achieves higher sensitivity and specificity than TopHat and SpliceMap on a set of simulated RNA-seq data. Experimental studies also support the accuracy of the algorithm. Splice junctions derived from eight breast cancer RNA-seq datasets recapitulated the extensiveness of alternative splicing on a global level as well as the differences between molecular subtypes of breast cancer. These combined results indicate that MapSplice is a highly accurate algorithm for the alignment of RNA-seq reads to splice junctions. Software download URL: http://www.netlab.uky.edu/p/bioinfo/MapSplice.

Publications

  1. MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.
    Cite this
    Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, He X, Mieczkowski P, Grimm SA, Perou CM, MacLeod JN, Chiang DY, Prins JF, Liu J, 2010-10-01 - Nucleic acids research

Credits

  1. Kai Wang
    Developer

    Department of Computer Science, University of Kentucky, United States of America

  2. Darshan Singh
    Developer

  3. Zheng Zeng
    Developer

  4. Stephen J Coleman
    Developer

  5. Yan Huang
    Developer

  6. Gleb L Savich
    Developer

  7. Xiaping He
    Developer

  8. Piotr Mieczkowski
    Developer

  9. Sara A Grimm
    Developer

  10. Charles M Perou
    Developer

  11. James N MacLeod
    Developer

  12. Derek Y Chiang
    Developer

  13. Jan F Prins
    Developer

  14. Jinze Liu
    Investigator

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Summary
AccessionBT006332
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByJinze Liu