SpliceTrap is a statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq data, with broad applications for the study of alternative splicing. SpliceTrap approaches to exon inclusion level estimation as a Bayesian inference problem. For every exon it quantifies the extent to which it is included, skipped or subjected to size variations due to alternative 3’/5’ splice sites or Intron Retention. In addition, SpliceTrap can quantify alternative splicing within a single cellular condition, with no need of a background set of reads.
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Wu J, Akerman M, Sun S, McCombie WR, Krainer AR, Zhang MQ (2011)
SpliceTrap: a method to quantify alternative splicing under single cellular conditions:
Bioinformatics 27, 3010-3016, doi:10.1093/bioinformatics/btr508