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Exon analysis is a powerful complement to traditional 3’ expression analysis, providing new opportunities to identify biologically relevant splicing patterns. Alternative splicing is already known to play a role in guiding developmental processes such as tissue differentiation (3), and changes in alternative splicing patterns have been associated with cancer and other diseases. As next-generation sequencing technologies expand in popularity, knowledge of common and rare alternative splicing events is likely to expand greatly, further increasing the size and complexity of these data sets. JMP Genomics meets this challenge with intelligent filtering capabilities to reduce large data sets to reliable results, and powerful analytics capable of distinguishing statistically relevant exon-level and transcript-level changes using any platform that may detect alternative splice events.