Error in methyl kit (differential methylation analysis) in R
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6 weeks ago
harshraje19 ▴ 40

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
epeigenetics methylation differential analysis R methylkit DNA • 96 views
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