WGBS Data Analysis
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Entering edit mode
7 months ago

Hi I am using the MethylKit package for DMC analysis. My files look like

Chr    base Strand coverage freqC freqT


1 chr21 5099187 + 4 100 0

2 chr21 5099198 + 6 83 17

3 chr21 5099210 + 8 100 0

4 chr21 5099273 + 8 87 13

5 chr21 5103338 + 7 100 0

6 chr21 5103413 + 11 100 0

library("methylKit")

file.list = list ("BCPool-Chr21.txt", "BCID1417-Chr21.txt")

myobj = methRead (file.list, sample.id = list ("BCPool-Chr21", "BCID1417-Chr21"), assembly = "hg38", treatment = c(1,0), context = "CpG", mincov=3)

meth1=unite(myobj, destrand=TRUE)

destranding...

uniting...

meth2=unite(myobj, destrand=FALSE)

uniting...

dim(meth1)

[1] 264297 10

dim(meth2)

[1] 264297 10

Here I can see that the “destrand” is not working. For TRUE and FALSE, both the cases return a file of the same dimension. Could you please let me know why it is happening and how can I correct it?

Regards

Shrinka Sen

DNA Methylation • 255 views
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Entering edit mode

Please do not take this as an offense but you are basically posting the same type of beginner-level questions towards WGBS with methylKit for almost 24 months now. Consider to get local help who sits with you and walks you through the analysis, or ask your PI to get a contractor who can guide you. I really say this in your best interest, but you seem lost in your analysis. This is essentilly the code you already posted on 24 month back "MethylKit" package for WGBS data and you still have trouble with it. Also consider changing to any other package if methylKit is not getting it done for you, but make sure that you make progress. An online community is not meant to guide you through a project.