Error in methyl kit (differential methylation analysis) in R
0
0
Entering edit mode
15 months 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 • 331 views
ADD COMMENT

Login before adding your answer.

Traffic: 2172 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6