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


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. 




coverage dss wgbs • 381 views
ADD COMMENTlink written 2.2 years ago by floriandeckert30
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 317 users visited in the last hour