strand info of array chips
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3.9 years ago
miaowzai ▴ 280

I'm trying to understand the strand info provided by this site: http://www.well.ox.ac.uk/~wrayner/strand/

I downloaded the InfiniumOmniExpress-24v1-2_A1-b37-strand file. In the .strand file, for example, there is a SNP rs11202902 at chr10:90693537, the strand column says β€œ-β€œ and the alleles column says β€œAT”. When I looked for this locus on the reference genome, it says the forward strand has A and reverse strand has T. This SNP rs11202902 is a variation from A to T mutation at the forward strand. I'm confused about the strand column and the alleles column in the .strand file. Shouldn't the strand be "+" for this SNP?

Does anyone who is familiar with the chip can explain to me? What exactly is the "alleles" (e.g. "AT", "AC", "CG", etc.) recorded in the column for each locus and how should I use the strand info in the file? Thanks a lot!

microarray strand ChIP-Seq • 999 views
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