Error in methyl kit (differential methylation analysis) in R

Question

[harshraje19]

Hello everyone, I am trying to perform the differential methylation analysis using the methyl kit but i got error message as "Error in methCall(read1 = location, type = "bam", nolap = nolap, minqual = minqual, : Unexpected cigar: M"

The detailed information about my R script is as below, can anyone help me to sort it out?

Thanks Raj

setwd("~/Desktop/sortedbam") library(methylKit) bam.file.list=list( "ST2_B1_sorted.bam","ST2_B2_sorted.bam","ST2_B3_sorted.bam","ST12_B1_sorted.bam","ST12_B2_sorted.bam","ST12_B3_sorted.bam")

myobj=processBismarkAln(bam.file.list,

• sample.id=list("test1","test2","test3","control1","control2","control3"),
• assembly="Edwards",
• save.folder = getwd(),
• save.context = c("CpG"),
• read.context = "CpG",
• nolap = FALSE,
• mincov = 10,
• minqual = 20,
• treatment=c(1,1,1,0,0,0),
• save.db = FALSE) Trying to process: ST2_B1_sorted.bam Using htslib. Error in methCall(read1 = location, type = "bam", nolap = nolap, minqual = minqual, : Unexpected cigar: M