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


The new Infinium MethylationEPIC v1.0 B5 Array Manifest File that was released in March 2020 (, 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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