I am conducting epigenetic aging clock research and need to align Illumina methylation array probes (27k, 450k, EPIC) to the hg38 genome assembly. I aim to learn robust methodological approaches for probe coordinate mapping rather than obtaining pre-made annotation files. Could anyone recommend key literature or detailed workflows that systematically describe the mapping process? Of course, any literature detailing direct methods for mapping legacy annotation files to hg38 would be especially helpful. Thank you.
•
written
by
huangyiming •
1 answer
SeSAme likely has what you want. It already has hg38 mappings for all of those platforms.
If you want to do it yourself, then yeah, probably look at the resource ATpoint provided.
Log in to answer this question.
its better if you ask the illumina tech support they can help for the mapping issue.
It it more than just aligning the fasta file with the probe sequences to a reference genome? Only difficulty is to decide what to do with imperfect matches, split- or other non-primary alignments. Maybe see https://www.ensembl.org/info/genome/microarray_probe_set_mapping.html for starters, despite it's probably expression arrays rather than genome arrays.