RNA modifications, especially methylation of the N6 position of adenosine （A）--m 6A, represent an emerging research frontier in RNA biology. With the rapid development of high-throughput sequencing technology, in-depth study of m 6A distribution and function relevance becomes feasible. However, a robust method to effectively identify m 6A-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 6A 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 6A regions from the background. Furthermore, MeRIP-PF also achieves gene annotation of m 6A 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.
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