Question: DSS CpG coverage threshold
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gravatar for floriandeckert
2.0 years ago by
floriandeckert30 wrote:

Hello! 

Since I do not have biological replicates I want to call DMRs with DSS. As far as I understand, first a basic smoothing is performed before using a beta-binominal GLM that takes biological and technical variance e.g. read-depth into account. 

I have to admit, that I have not fully understand the theoretical background -- that is probably why I have to ask the following question: Prior analysis, should I filter out CpGs with low coverage or should I explicitly not filter any CpGs? 

I thought I have read that DSS is ignoring CpGs with coverage < 5 but I can not find that reference no more. But that would be also a threshold I am considering to choose -- If necessary or recommended. 

Any advice highly appreciated. 

Best

 

 

coverage dss wgbs • 357 views
ADD COMMENTlink written 2.0 years ago by floriandeckert30
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