Question: EPIC methylation manifest GRch38 query
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gravatar for prasundutta87
8 weeks ago by
prasundutta87360
prasundutta87360 wrote:

Hi,

The new Infinium MethylationEPIC v1.0 B5 Array Manifest File that was released in March 2020 (https://emea.support.illumina.com/array/array_kits/infinium-methylationepic-beadchip-kit/downloads.html), finally has the start and end positions for hg38 genome for each probe. For example, for one probe, it is chr19:5236004-5236006. which is in the form of CHR_hg38 : Start_hg38 - End_hg38

I am annotating my processed EPIC array IDAT files using this manifest. (Processing done using minfi)

My question is if it is 0-based on 1-based coordinates? I did not find the information anywhere. Does the position signify 'CG' dinucleotide position? If it is 1-based, then it seems to indicate a range of trinucleotides. But if 0-based, it will indicate a range of dinucleotide ('CG').

I want to convert it into a Bedgraph format, i.e. 0-based coordinate system, so wanted to be sure of this.

Regards, Prasun

ADD COMMENTlink written 8 weeks ago by prasundutta87360

Found the answer myself, it turns out that its 0-based, however, when pasted in UCSC genome browser, 3 nucleotides come up, but that's because the browser runs on the 1-based coordinate system.

ADD REPLYlink written 7 weeks ago by prasundutta87360
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