Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605 and Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Bioinformatics. 2013 Oct 1;29(19):2485-6. doi: 10.1093/bioinformatics/btt428. Epub 2013 Aug 8.
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.
ASPeak is implemented in Perl as a complete pipeline that takes bedGraph files as input. ASPeak implementation is freely available at https://sourceforge.net/projects/as-peak under the GNU General Public License. ASPeak can be run on a personal computer, yet is designed to be easily parallelizable. ASPeak can also run on high performance computing clusters providing efficient speedup. The documentation and user manual can be obtained from http://master.dl.sourceforge.net/project/as-peak/manual.pdf.
与 DNA 不同，RNA 的丰度可以变化几个数量级。因此，从高通量测序数据中识别 RNA-蛋白质结合位点提出了独特的挑战。尽管 ChIP-Seq 数据中的峰识别已经得到了广泛的研究，但针对 RNA 结合蛋白的类似数据集的峰调用，生物信息学工具还很少。在这里，我们描述了 ASPeak（丰度敏感峰检测算法），这是我们之前应用于串联实验中外显子连接复合物 RNA 免疫沉淀中检测峰的算法的实现。我们的峰检测算法产生了严格而稳健的目标集，能够进行敏感的基序发现和下游功能分析。
ASPeak 是用 Perl 实现的，作为一个完整的管道，以 bedGraph 文件作为输入。ASPeak 的实现可在 https://sourceforge.net/projects/as-peak 下根据 GNU 通用公共许可证免费获得。ASPeak 可以在个人计算机上运行，但设计为易于并行化。ASPeak 也可以在高性能计算集群上运行，提供高效的加速。文档和用户手册可从 http://master.dl.sourceforge.net/project/as-peak/manual.pdf 获得。
