RNA modifications, especially methylation of the N6 position of adenosine (A)—m6A, represent an emerging research frontier in RNA biology.MeRIP-Seq, which combines m6A-specific methylated RNA immunoprecipitation with next-generation sequencing (NGS) technology, can catch the modifications in whole transcriptome.We developed MeRIP-PF (http://software.big.ac.cn/MeRIP-PF.html) which can detect m6A modification regions by statistical methods based on comparing reads distribution between control samples and treated samples.