Question: Using CEAS with canine methylation data
0
gravatar for Saad Khan
5.8 years ago by
Saad Khan400
United States
Saad Khan400 wrote:

Hi ,

I am working on Dog genome MEDIP-seq DNA methylation data.I came across CEAS (http://liulab.dfci.harvard.edu/CEAS/usermanual.html)

I was wondering if there is any way I can use it with Dog genome. Although it is explicitly used for chip-seq data but I have seen people have used it for Medip-seq data as well. As shown in this pipeline (http://life.tongji.edu.cn/meqa/)

dog ceas methylation medip-seq • 1.6k views
ADD COMMENTlink modified 5.7 years ago by Biostar ♦♦ 20 • written 5.8 years ago by Saad Khan400

Having never looked, how well annotated is the dog genome? If its annotation is OK then there's no reason you can't use CEAS (just give it the estimated methylation levels from MEDIPS/batman/etc.).

ADD REPLYlink written 5.8 years ago by Devon Ryan95k

Its not comparable to Human annotation although considerable annotation can be obtained using (Ensembl API). I was more interested in accessing the content of sql file for CEAS and if there is a way to develop that. The sql file for Human is available here (http://liulab.dfci.harvard.edu/CEAS/src/hg19.refGene.gz ). I have tried to contact the authors but as to how can I generate it for other species but haven't heard from them.  Thus any insights from you would be helpful

ADD REPLYlink modified 5.8 years ago by Devon Ryan95k • written 5.8 years ago by Saad Khan400
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