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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 two questions are:
Q1) Does anyone has a suggestion as an alternative to BiSeq? I was also looking into MethylKit but saw it has not been updated since 2013 so not quite sure if it is the best option.
Q2) 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 do have plot the "coverage histogram" for each sample. See an example in the png attached. And now my last question related to this plot:
Q3) Would you expect this distribution? As you can see there are very high coverage values (I have found around 4k higher than 200, with maximum value of 16k - this located in chromosome 21).
If you could bring some light here I would really appreciate. Many thanks in advance!
Maria
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 two questions are:
Q1) Does anyone has a suggestion as an alternative to BiSeq? I was also looking into MethylKit but saw it has not been updated since 2013 so not quite sure if it is the best option.
Q2) 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 do have plot the "coverage histogram" for each sample. See an example in the png attached. And now my last question related to this plot:
Q3) Would you expect this distribution? As you can see there are very high coverage values (I have found around 4k higher than 200, with maximum value of 16k - this located in chromosome 21).
If you could bring some light here I would really appreciate. Many thanks in advance!
Maria