New Splice Junction Mapping Tool – MapSplice

The accurate mapping of reads that span splice junctions is a critical component of all analytic techniques that work with RNA-seq data. Here is 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.

Included is a demonstration that MapSplice achieves higher sensitivity and specificity than TopHat and SpliceMap on a set of simulated RNA-seq data.

Additional experimental results… 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.

Software download URL:

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) MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res [Epub ahead of print]. [article]