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Can I use UCSC genome browser to annotate Epic data

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
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updated by BiostarGuardianAngel • BiostarGuardianAngel • written by AHW • AHW

Isn't Illumina the source for their 450k array probe data?

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written by Alex Reynolds Alex Reynolds

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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written by Friederike Friederike

1 answer

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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written by BiostarGuardianAngel • BiostarGuardianAngel

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