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which is good to study methylation among breast cancer patients; ChIP-Seq and Whole-genome bisulfite sequencing?

Dear colleagues and Senior Members,

I'm designing a study to determine the epigenetic landscape among breast cancer patients. Can anyone advise on which technique would to appropriate or best?; ChIP-Seq and Whole-genome bisulfite sequencing?

Thanks Sam

chip-seq methylation bisulfite sequencing
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written by Alewa Alewa

This feels more like a biology question... You may try seqanswers.com? I guess it depends on which aspects are more important to you, methylation or histone marks or what. You may be able to find some public data to get you started.

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written by Madelaine Gogol Madelaine Gogol

Two assays are very different and which one is best it depends on the question you are asking. If you have the option for only one, you can compare the cost, data size, computational requirement for downstream analysis etc.

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written by Rashedul Islam Rashedul Islam

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