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09-07-2020, 03:26 AM
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Junior Member
Location: Victoria Join Date: Sep 2020
Posts: 1
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Analysis WGBS data question
Hello
I'm analyzing WGBS (bulk) data from ENCODE project. I would like to know how do many researchers analyze WGBS data. When I extracted CpG sites having > 10 coverage on 20 samples, CpG sites having >10 coverage on more samples than 70% of all samples are approx. 30 % of all CpG sites. so if one region be focused, the methylation information of the region contains many missing value. I think that imputation can not be applied, because of numerousness of missing value. So should I treat average methylation rate on each focused regions and compare with average methylation rate ? and additional question is that How bacth effect and blood contamination effect are removed? I'm beginner. so I need information (paper, web sites shows analysis process) I hope your help thank you |
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