Illumina EPIC array manifest file header

Question

[현호]

Hi,

Now im trying to do liftover(hg19 to hg38) my DMP result with illumina manifest file.

But, I have a question about infinium-methylationepic-v-1-0-b5-manifest-file.

In version B5, start and end site in hg38 were added.

I wonder why they give 'region' for each CpG 'site' while other column, hg19 or hg18, give only one position.

How can i interpret it?

I already saw this post in Biostar but i still dont know why. You can see the manifest file in this link.

Could you give me some advise?

Thanks.

Answer 1

[Molin]

Hi, I have the same question and I just figured it out recently. it turns out that for 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.