title: MeRIP-PF: an easy-to-use pipeline for high-resolution peak-finding in MeRIP-Seq data.
abstract: RNA modifications, especially methylation of the N(6) position of adenosine (A)-m(6)A, represent an emerging research frontier in RNA biology. With the rapid development of high-throughput sequencing technology, in-depth study of m(6)A distribution and function relevance becomes feasible. However, a robust method to effectively identify m(6)A-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 m(6)A region based on the difference of read distribution when compared to the controls and also calculates false discovery rate (FDR) as a cut off to differentiate reliable m(6)A regions from the background. Furthermore, MeRIP-PF also achieves gene annotation of m(6)A 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.
authors: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
authors: Yuli
authors: Y
authors: Li
authors: Shuhui
authors: S
authors: Song
authors: Cuiping
authors: C
authors: Li
authors: Jun
authors: J
authors: Yu
mesh_terms: D000241:Adenosine / Q000235:genetics*; D000818:Animals; D008745:Methylation; D051379:Mice; D058977:Molecular Sequence Annotation; D012313:RNA / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012333:RNA, Messenger; D012313:RNA; D000241:Adenosine