I'm running DMR analysis in SeqMonk using context specific methylation extraction files produced in Bismark. I've created probes using the read position probe generator and have quantified using the Bisulfite Methylation Quantitation Pipeline.
When I run the Logistic Regression statistical test for replicate data, many areas of interest are identified, which I can then scroll and see some obvious DMRs of interest using the track display. By obvious, I mean there are regions which are highly methylated in one replicate group (value >50) that lack any methylation in the other group. This is not due to low coverage; I have achieved 80x genome coverage.
However, when I use the "Filter on Value Differences --> Individual probes" to identify DMRs of >= 20% difference in methylation, no probes are returned.
Can anyone suggest why these regions are not being picked up by the filter?
**I do not have this problem when I use coverage files from Bismark. However, I don't have the methylation by sequence context information if I rely on the .cov files for this analysis, which is why I'm using the files produced by the methylation extraction step in Bismark.
When I run the Logistic Regression statistical test for replicate data, many areas of interest are identified, which I can then scroll and see some obvious DMRs of interest using the track display. By obvious, I mean there are regions which are highly methylated in one replicate group (value >50) that lack any methylation in the other group. This is not due to low coverage; I have achieved 80x genome coverage.
However, when I use the "Filter on Value Differences --> Individual probes" to identify DMRs of >= 20% difference in methylation, no probes are returned.
Can anyone suggest why these regions are not being picked up by the filter?
**I do not have this problem when I use coverage files from Bismark. However, I don't have the methylation by sequence context information if I rely on the .cov files for this analysis, which is why I'm using the files produced by the methylation extraction step in Bismark.
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