Hi Maria, I don't know SAAP-BS, but from the column names I suppose that you are right: totalC corresponds to totalReads and methC and to methReads. CpG sites with very high coverages are to be expected. At least I have never seen an RRBS data set without it. In the BiSeq pipeline it is suggested to limit the coverage, e.g., to the 0.9 quantile (page 15): http://bioconductor.org/packages/release/bioc/vignettes/BiSeq/inst/doc/BiSeq.pdf Cheers, Katja ----- Original Message ----- > From: "maria.maqueda [bioc]" <noreply@bioconductor.org> > To: katjah@stanford.edu > Sent: Tuesday, April 28, 2015 8:53:15 AM > Subject: [bioc] SAAP-BS data analysis (RRBS) - BiSeq use and Coverage > Histogram > Activity on a post you are following on support.bioconductor.org > User maria.maqueda wrote Question: SAAP-BS data analysis (RRBS) - BiSeq use > and Coverage Histogram : > Hello all, > 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! > Maria > You may reply via email or visit SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram