ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq
ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq
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DOI：
10.1093/bioinformatics/btt428
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发表时间：
2013-10-01
期刊：
影响因子：
5.8
通讯作者：
Cenik, Can
中科院分区：
文献类型：
--
作者：
Kucukural, Alper;Oezadam, Hakan;Cenik, Can
与 DNA 不同，RNA 丰度可以变化几个数量级。因此，从高通量测序数据中鉴定 RNA-蛋白质结合位点提出了独特的挑战。尽管 ChIP-Seq 数据中的峰识别已被广泛探索，但很少有专门针对 RNA 结合蛋白的类似数据集进行峰识别的生物信息学工具。在这里，我们描述了 ASPeak（丰度敏感峰检测算法），这是我们之前在串联实验中用于检测外显子连接复合物 RNA 免疫沉淀中的峰的算法的实现。我们的峰检测算法可产生严格且稳健的目标集，从而实现灵敏的基序发现和下游功能分析。
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. Although peak identification in ChIP-Seq data has been extensively explored, there are few bioinformatics tools tailored for peak calling on analogous datasets for RNA-binding proteins. Here we describe ASPeak (abundance sensitive peak detection algorithm), an implementation of an algorithm that we previously applied to detect peaks in exon junction complex RNA immunoprecipitation in tandem experiments. Our peak detection algorithm yields stringent and robust target sets enabling sensitive motif finding and downstream functional analyses.