Infinium MethylationEPIC Annotation under hg38

Question

[Molin]

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

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?

Answer 1

[Molin]

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.