I am struggling with the DMR analysis of some RRBS data already processed with SAAP-BS program. I do not have the SAM/BAM files, just a merged csv file with the methylC, totalC and Ratio per sample and CpG site (around 2.5M).
I am new to this type of analysis (previously worked with expression analysis) and I have decided to use BiSeq for obtaining DMR. My first question is: I have to create by hand the BSraw object, is "totalReads" equivalent to "totalC" and "methReads" equivalent to "methC"?
On the other hand I have supposed that "totalC" from SAAP-BS report is equivalent to the coverage mentioned in RRBS/WGBS publications. Assuming my supposition is right (if not, please correct me!!!), I have found there are very high coverage values (up to maximum value of 16k - this located in chromosome 21, around 4k CpG sites with coverage > 200). Is this to be expected?
If you could bring some light here I would really appreciate. Many thanks in advance!
Many thanks for you quick answer! Yes, I saw the very high coverage filtering in the BiSeq filtering, thanks for referring.