m6A-seq_analysis_workflow

github：https://github.com/scottzijiezhang/m6A-seq_analysis_workflow

R包：scottzijiezhang/m6Amonster: Analyze m6A seq data version 0.1.2 from GitHub

比对成bam

library(m6Amonster)

samplenames = c("sample1","sample2","sample3")

monster <- countReads(samplenames = samplenames,

                    gtf = "~/Database/genome/hg38/hg38_UCSC.gtf",

                    bamFolder = "/home/xxx/project1/bam_files",

                    outputDir =  "/home/xxx/project1/fisherPeak",

                    modification = "m6A",

                    binSize = 50,

                    threads = 6

)

monster <- callPeakFisher(monster, min_counts = 15, peak_cutoff_fdr = 0.05 , peak_cutoff_oddRatio = 1, threads = 6)