Unlike DNA, RNA abundances can vary over several orders of magnitude. Thus identification of RNA-protein binding sites from high throughput sequencing data presents unique challenges. While peak identification in CHIP-Seq data has been extensively explored, there are few bioinformatics tools tailored to peak calling on the analogous datasets for RNA-binding proteins. Here we describe ASPeak, an implementation of an algorithm that we previously applied to detect peaks in Exon Junction Complex (EJC) RNA immunoprecipitation in tandem (RIPiT) experiments. Our peak detection algorithm yields stringent and robust target sets enabling sensitive motif finding and downstream functional analyses.
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