Map to get cpg probe id provided chr, start and end position
Hi, I have this data from : https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE69894. Here is. a small subsample of the data:
chr start end cpg_id CD14_1 CD14_2 CD14_3 WholeBlood Tonsil_1 CD14_4 ... CD8N_2 PBMC_2 CD4M_3 CD4N_3 CD8N_3 PBMC_3 Cortex_1 GanglionicEminence_1 Cortex_2 GanglionicEminence_2
0 chr1 10468 10470 chr1.1 0.95 0.46 0.95 0.95 0.91 0.95 ... 0.91 0.91 0.95 0.91 0.91 0.91 0.95 0.46 0.95 0.91
1 chr1 10470 10472 chr1.2 0.98 0.46 0.98 0.95 0.94 0.95 ... 0.94 0.91 0.95 0.91 0.91 0.94 0.98 0.46 0.98 0.91
2 chr1 10483 10485 chr1.3 0.98 0.46 0.98 0.95 0.93 0.98 ... 0.91 0.94 0.94 0.94 0.94 0.91 0.96 0.46 0.91 0.94
My aim is to find the corresponding Cg probe id from human methylation 450k (Hg19). I have information about chromosome and genomic coordinates which I obtained from 'The Infinium HumanMethylation450K v1.2 manifest file. There is a problem in mapping as there is no common column in both files.
PS: in short I have to map and find the cpg probe id related to chr, start and end position.
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The link you provided above is for sequencing data (not arrays). And you want to map these sequence intervals/ID's onto a methylation array. Is that correct?
Yes, I have to get the Cg probe ids corresponding to these chromosomes.