Problem in working with BiSeq - BSraw
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@ahmadmoousavi-14701
Last seen 2.8 years ago

Hi

I wanted to use BiSeq for my RRBS data but I little confused in how to make BSraw object.

I have 20 RRBS samples in 7 groups, my genome is Mouse (mm10) and I would like to find all DMR in all chromosomes.

Do you have any idea about creating BSraw in default way? because I've tried many times but I got little progress in it.

BSraw(metadata = metadata,

rowRanges = rowRanges,

colData = colData,

totalReads = totalReads,

methReads = methReads)

 

Thanks

 

dna methylation biseq • 497 views
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@gordon-smyth
Last seen 12 minutes ago
WEHI, Melbourne, Australia

The BiSeq package provides a function readBismark() that reads Bismark coverage files and creates a BSraw object for you. What have you tried if not that?

Alternatively, if you're willing to try other methods, there is a detailed workflow for detecting differential methylation from RRBS data at:

https://f1000research.com/articles/6-2055

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