Comparing Illumina with Affymetrix data

Question

[alcar]

I have data from a 50k Illumina bovine chip and data from a 600k Affymetrix bovine chip and I would like to do analyses on the SNPs that are common to both chips.

Do you know a way to get all the common SNPs from both chips since Illumina and Affymetrix don't use the same SNP IDs and genome assembly?

Thank you

Answer 1

[Rashedul Islam]

Two relevant discussion on the question:

1. Mapping Illumina Snp Ids To Rs Ids.

2. rs id comparison between genome version or build.