MeRIP-PF:An Easy-to-use Pipeline for High-resolution Peak-finding in MeRIP-Seq Data  

作　　者：Yuli Li Shuhui Song Cuiping Li Jun Yu 

机构地区：[1]CAS Key Laboratory of Genome Sciences and Information,Beijing Institute of Genomics,Chinese Academy of Sciences [2]University of Chinese Academy of Sciences [3]Core Genomic Facility,Beijing Institute of Genomics,Chinese Academy of Sciences

出　　处：《Genomics, Proteomics & Bioinformatics》2013年第1期72-75,共4页基因组蛋白质组与生物信息学报（英文版）

基　　金：supported by Grants from the Ministry of Science and Technology of China (Grant No. 2011CB944100) to JY;the Natural Science Foundation (Grant No. 30900831 and 31271372);Beijing Nova Program (Grant No. Z121105002512060)to SS

摘　　要：RNA modifications, especially methylation of the N6 position of adenosine （A）--m6A, rep- resent an emerging research frontier in RNA biology. With the rapid development of high-throughput sequencing technology, in-depth study of m6A distribution and function relevance becomes feasible. However, a robust method to effectively identify m6A-modified regions has not been available yet. Here, we present a novel high-efficiency and user-friendly analysis pipeline called MeRIP-PF for the signal identification of MeRIP-Seq data in reference to controls. MeRIP-PF provides a statistical P-value for each identified m6A region based on the difference of read distribution when compared to the con- trols and also calculates false discovery rate （FDR） as a cut offto differentiate reliable m6A regions from the background. Furthermore, MeRIP-PF also achieves gene annotation ofm6A signals or peaks and produce outputs in both XLS and graphical format, which are useful for further study. MeRIP-PF is implemented in Perl and is freely available at http：//software.big.ac.cn/MeRIP-PF.html.RNA modifications, especially methylation of the N6 position of adenosine （A）--m6A, rep- resent an emerging research frontier in RNA biology. With the rapid development of high-throughput sequencing technology, in-depth study of m6A distribution and function relevance becomes feasible. However, a robust method to effectively identify m6A-modified regions has not been available yet. Here, we present a novel high-efficiency and user-friendly analysis pipeline called MeRIP-PF for the signal identification of MeRIP-Seq data in reference to controls. MeRIP-PF provides a statistical P-value for each identified m6A region based on the difference of read distribution when compared to the con- trols and also calculates false discovery rate （FDR） as a cut offto differentiate reliable m6A regions from the background. Furthermore, MeRIP-PF also achieves gene annotation ofm6A signals or peaks and produce outputs in both XLS and graphical format, which are useful for further study. MeRIP-PF is implemented in Perl and is freely available at http：//software.big.ac.cn/MeRIP-PF.html.

关 键 词：RNA modification m 6A Peak finding MeRIP-Seq 

分 类 号：Q811.4[生物学—生物工程]