analysing bismark.cov.gz files

Question

[adR]

Hi all,

I have 100 whole bisulfate sequenced samples and generated 100 bismark.cov.gz files following the Bismark pipeline. I want to do differential methylation analysis as these samples have four groups.

When I open each bismark.cov.gz file, I see six columns and don't know which column to use to combine all the files to generate a single data frame. I use the R programming language for the analysis, and I would like to get some feedback or a pipeline or packages designed for this type of analysis.

Best, ADR

[Basti]

You may have a look at this tutorial : https://bioconductor.org/packages/release/bioc/vignettes/dmrseq/inst/doc/dmrseq.html

[adR]

Thank for your suggestion but reading 100 files as you could see below turns error.

file.list = c("/user/ad/A.bismark.cov.gz", "user/ad/B.bismark.cov.gz", "user/ad/C.bismark.cov.gz", "user/ad/D.bismark.cov.gz", "user/ad/E.bismark.cov.gz", "user/ad/F.bismark.cov.gz")

bismarkBSseq <- read.bismark(file.list, rmZeroCov = TRUE, strandCollapse = FALSE, verbose = TRUE)

here is the errors:

[read.bismark] Parsing files and constructing valid loci ... Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'unique': long vectors not supported yet: /Volumes/Builds/R4/R-4.2.3/src/main/memory.c:3885

do you have any idea what would be the cause?

Thank you!