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how to change the strand?

Hello, I am preparing imputation for Affy 5.0 array data (Plink files).
These are annotation files from Affymatrx and I have to correct all strand to 'forward', as you know.
I know I should make an RS ID list files but I'm not sure what information I should keep.
I will use PLINK with --flip option.
Should I keep the "-" strand or "reverse" for my list?

Thank you

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snp strand dbsnp imputation
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updated by Kevin Blighe Kevin Blighe • written by nayeona.hi nayeona.hi

1 answer

What is your ultimate intention for this data? Generally, though, I would 'flip' to the coding / positive / plus / + / sense strand. You can see one reason why, here (point 6): Produce PCA bi-plot for 1000 Genomes Phase III - Version 2

Kevin

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written by Kevin Blighe Kevin Blighe

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