title: SpliceTrap: a method to quantify alternative splicing under single cellular conditions.
abstract: BACKGROUND
  Alternative splicing (AS) is a pre-mRNA maturation process leading to the expression of multiple mRNA variants from the same primary transcript. More than 90% of human genes are expressed via AS. Therefore, quantifying the inclusion level of every exon is crucial for generating accurate transcriptomic maps and studying the regulation of AS.
  
  
  RESULTS
  Here we introduce SpliceTrap, a method to quantify exon inclusion levels using paired-end RNA-seq data. Unlike other tools, which focus on full-length transcript isoforms, SpliceTrap approaches the expression-level estimation of each exon as an independent Bayesian inference problem. In addition, SpliceTrap can identify major classes of alternative splicing events under a single cellular condition, without requiring a background set of reads to estimate relative splicing changes. We tested SpliceTrap both by simulation and real data analysis, and compared it to state-of-the-art tools for transcript quantification. SpliceTrap demonstrated improved accuracy, robustness and reliability in quantifying exon-inclusion ratios.
  
  
  CONCLUSIONS
  SpliceTrap is a useful tool to study alternative splicing regulation, especially for accurate quantification of local exon-inclusion ratios from RNA-seq data.
  
  
  METHODS
  SpliceTrap can be implemented online through the CSH Galaxy server http://cancan.cshl.edu/splicetrap and is also available for download and installation at http://rulai.cshl.edu/splicetrap/.
  
  
  BACKGROUND
  michael.zhang@utdallas.edu.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
authors: Jie
authors: J
authors: Wu
authors: Martin
authors: M
authors: Akerman
authors: Shuying
authors: S
authors: Sun
authors: W Richard
authors: WR
authors: McCombie
authors: Adrian R
authors: AR
authors: Krainer
authors: Michael Q
authors: MQ
authors: Zhang
mesh_terms: D017398:Alternative Splicing; D001499:Bayes Theorem; D005091:Exons; D006801:Humans; D017423:Sequence Analysis, RNA; D012984:Software