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Genomics Proteomics Bioinformatics. 2013 Feb;11(1):72-5. doi: 10.1016/j.gpb.2013.01.002. Epub 2013 Jan 20.

MeRIP-PF: an easy-to-use pipeline for high-resolution peak-finding in MeRIP-Seq data.

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1
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.

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.

PMID:
23434047
PMCID:
PMC4357668
DOI:
10.1016/j.gpb.2013.01.002
[Indexed for MEDLINE]
Free PMC Article
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