How to analysis WGBS data

yu_chem · 04-15-2018, 11:01 AM

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

penathograymatter · 04-15-2018, 11:15 PM

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04-15-2018, 11:01 AM	#1
yu_chem Member Location: Japan Join Date: Mar 2015 Posts: 22	How to analysis WGBS data 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

04-15-2018, 11:15 PM	#2
penathograymatter Junior Member Location: usa Join Date: Apr 2018 Posts: 1	Pentaho Consulting Services Pentaho Consulting Services : GrayMatter is World's Largest Pentaho Consulting company. GrayMatter is also the World's largest pentaho workshop that helps you develop, design and implement your analytics with Pentaho business analytics, Pentaho Support tools and other pentaho related services. Visit:https://pentaho.graymatter.co.in/ __________________ Pentaho