DSS CpG coverage threshold
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@floriandeckert-13733
Last seen 10 weeks ago
Austria

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

 

 

DSS WGBS coverage • 1.6k views
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Might be a bit late for the original poster :') but in case anyone else is wondering, the DSS user guide says:

Q: Do I need to filter out CpG sites with low or no coverage? A: No. DSS will take care of the coverage depth information. The depth will be factored into the statistical computation.

https://bioconductor.org/packages/release/bioc/vignettes/DSS/inst/doc/DSS.html

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