Can I use UCSC genome browser to annotate Epic data
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20 months ago
AHW ▴ 40

I have Epic methylation data and was just trying to find annotations for CpGs, however, I don't find some CpGs in the genome browser. I can find some CpGs which I believe may be from 450K data. I would like to know if UCSC browser has Epic CpG annotations.

I already have Illumina annotation file for Epic, I am trying to cross-check the annotations.

annotation • 583 views
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Isn't Illumina the source for their 450k array probe data?

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I don't get what you mean by "I don't find some CpGs in the genome browser". The Genome Browser provides the entire genome and if you select the correct version, it should, in fact, display more CpGs than those on the array. What type of format are you looking for and how exactly do you go about searching for the CpGs?

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3 months ago

Not sure if this helps but there is a UCSC_Islands_Name column in format like "chr16:53468284-53469209" using the code below?

BiocManager::install("ChAMPdata")
library(ChAMPdata)
data(probe.features.epic)
View(probe.features)
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