I’m trying to use the Infinium Human Methylation BeadChip workflow in Galaxy with idat files from an Illumina EPIC chip. It’s based on Minfi, which I usually run in Rstudio but wanted to give it a try. It’s ok with the idat files ant the phenotype table, but then I’m asked for a GTF Genome Table (in the example wgEncodeHaibMethyl450Gm12878SitesRep1). What should this genome table be for an EPIC chip?
Instructions are in the tutorial associated with the workflow in this section: