The emergence of next-generation high-throughput RNA sequencing (RNA-Seq) provides tremendous opportunities for researchers to analyze alternative splicing on a genome-wide scale. However, accurate identification of alternative splicing events from RNA-Seq data has remained an unresolved challenge in next-generation sequencing (NGS) studies. Identifying exon skipping (ES) events is an essential part in genome-wide alternative splicing event identification. In this paper, we propose a novel method ESFinder, a random forest classifier to identify ES events from RNA-Seq data. ESFinder conducts thorough studies on predicting features and figures out proper features according to their relevance for ES event identification. Experimental results on real human skeletal muscle and brain RNA-Seq data show that ESFinder could effectively predict ES events with high predictive accuracy. The codes of ESFinder are available at http://mlg.hit.edu.cn/ybai/ES/ESFinder.html.
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