title: MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.
abstract: 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.
authors.affiliation: Department of Computer Science, University of Kentucky, Lexington, KY 40506, USA.
authors.forename: Kai
authors.initials: K
authors.lastname: Wang
authors.forename: Darshan
authors.initials: D
authors.lastname: Singh
authors.forename: Zheng
authors.initials: Z
authors.lastname: Zeng
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Coleman
authors.forename: Yan
authors.initials: Y
authors.lastname: Huang
authors.forename: Gleb L
authors.initials: GL
authors.lastname: Savich
authors.forename: Xiaping
authors.initials: X
authors.lastname: He
authors.forename: Piotr
authors.initials: P
authors.lastname: Mieczkowski
authors.forename: Sara A
authors.initials: SA
authors.lastname: Grimm
authors.forename: Charles M
authors.initials: CM
authors.lastname: Perou
authors.forename: James N
authors.initials: JN
authors.lastname: MacLeod
authors.forename: Derek Y
authors.initials: DY
authors.lastname: Chiang
authors.forename: Jan F
authors.initials: JF
authors.lastname: Prins
authors.forename: Jinze
authors.initials: J
authors.lastname: Liu
mesh_terms: D000465:Algorithms; D017398:Alternative Splicing; D001943:Breast Neoplasms / Q000235:genetics; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D022821:RNA Splice Sites; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D022821:RNA Splice Sites
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