Hi, I am trying to identify Illumina HT12v4 probes that contain a common SNP. I have downloaded the gene expression annotation file from Illumina.com and a list of SNPs with their genomic location from dbsnp (hg18). As a sanity check I have compared the probe coordinates given by Illumina with the probe coordinates given by the UCSC Genome Browser for hg18. Unfortunately probe coordinates between Illumina and UCSC do not match all the time (by manually checking a few I got about 30% mismatch). The probe sequences given by Illumina and UCSC perfectly match 100% of the cases. What am I missing here? Am I correct in using Illumina probe coordinates and dbsnp hg18 coordinates or I should remap my probe sequences to hg18 before checking for overlap with dbsnp? If so can you suggest me a tool to do that, I have about 48,000 probes.
Thanks a lot in advance Any help will be greatly appreciated
The explanation could be that the genome build for the probes was not hg18
It says here in the product description that HT12V14 probes were derived from Reference Sequence (NCBI) RefSeq Release 38 (November 7, 2009) and other sources. So you cannot expect these probes to have identical probe coordinates to that of hg18.