Infinium MethylationEPIC Annotation under hg38
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6 weeks ago
Molin • 0

Hi! I'm recently working on Infinium MethylationEPIC data for eQTM analysis. When I tried to map the Cis-Methylation site to Gene, I met a problem. Since I have Gene expression data aligned to hg38 reference, So I need also find the methylation probe location under hg38. I downloaded a manifest file from Illumina support page:(https://support.illumina.com/downloads/infinium-methylationepic-v1-0-product-files.html)

Infinium MethylationEPIC v1.0 B5 Manifest File (CSV Format)

And it has the annotation information for all the probes under hg37 and hg38 hg37 info hg38 info

But for hg38, each probe has a start_location and end_location, with 3 bp long which is weird. So Can anyone help me with why the new annotation for each probe is 3 bp long, shall I use the mid?

Microarray Methylation • 261 views
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Entering edit mode
5 weeks ago
Molin • 0

It turns out that the hg38 manifest file, it provides location information based on the 0-ordinates system which means it starts from 0 and it's left close right open intervals.

for example, start 100, end 102 means the CpG site is from 100 to 101, took 2 bp. the reason why it takes 2 bp I think is because it records "CG" 2 nucleotides. So compared to the older manifest files, only the start position should be used.

Hope this can help.

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