Hello,

Recently I received methylation call files from my last RRBS and RRoxBS analysis and I would like to analyse them with the Methylkit R package.

I have executed the next script:

WT8_BS <- read_table("T:/RROxBS/WT8_BS/methylcall.CpG.WT8_BS.1x.txt", col_names = FALSE)
KO8_BS <- read_table("T:/RROxBS/KO8_BS/methylcall.CpG.KO8_BS.1x.txt", col_names = FALSE)
WT8_BS <- select(WT8_BS, -X8, -X9)
KO8_BS <- select(KO8_BS, -X8, -X9)

names(WT8_BS) <- c("chrBase", "chr", "base", "strand", "coverage", "freqC", "freqT")
names(KO8_BS) <- c("chrBase", "chr", "base", "strand", "coverage", "freqC", "freqT")

files <- list(WT8_BS, KO8_BS)

WT8 <- methRead(files, 
                sample.id = list("WT8_BS", "KO8_BS"),
                assembly = "mm10",
                treatment = c(0,1),
                context = "CpG",
                dbtype = "tabix",
                dbdir = "methylDB"
                )

My problem is that when I execute the last step it never ends, it remains like the image:

I do not know which could be the problem. I also tried to read the methylation call files and store them as flat file database as it says in mehtylkit manual, but it does not work either.

Thanks in advance!