I am lost here.
I ran alignment with BWA-Meth and got methylKit output from methylDackel.
The output file has 7 columns
chrBase, chr, base, strand, coverage, freqC, freqT
I imported the files into R and tried to run MethylKit, but once I created the file.list and run
> myobj=methRead(file.list,
+
sample.id=list("DMSO1","DMSO2","DMSO3","SAM1","SAM2","SAM3"),
+ assembly="hg38",
+ treatment=c(1,1,1,0,0,0),
+ context="CpG",
+ mincov = 10,
+ dbtype = "tabix",
+ dbdir = "methylDB"
+ )
It ran for a like 2 hours and all I get is
Received list of locations.
creating directory methylDB ...
Error in file.exists(filepath) : invalid 'file' argument.
Should I not import the Dataset using From Text (base) and tab delineated option?
Am I missing hg38 assembly?
When I ran MethylDackel, I did extensive trimming with mbias. Could that have caused the problem? Should I lower mincov to 3 or something?
What does invalid file mean? Any help will be immensely appreciated.
Thanks,