CpG coverage of BS-seq ?

Question

[hxlei613]

Hello,I have a question about the CpG coverage of BS-seq. In general many papers would say that how many CpGs are covered by their RRBS experiments. I wonder what is the definition of the CpG. Here is an example:

• 5' ---CG---3'
• 3' ---GC---5'

My question is : Are there two CpGs or just one CpG ? (Just want to know if CpGs are distinguished by strand).

Also,I wonder if there are "gold standards" for RRBS, such as the experiment can be thought successful if there are at least millions of CpGs are covered, the percentage of 5x(or 8x or 10x) CpG should exceeds 90% (or 80% or else). Thanks for any comments.

Answer 1

[Aerval]

CpG usually means the CpG dinucleotide (and is afaik specified otherwise if not). When you use bsseqs getCov you get the number of + and - strand reads. (I have no idea about RRBS as I am working with WGBS)

[hxlei613]

Hi, I updated my question to make sure I have expressed myself clearly. Thank you very much!

[Aerval]

Sorry if I misused the term dinucleotide, I meant both cytosines in a CpG double strand site. So one CpG.