how to change the strand?

Question

[nayeona.hi]

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

Answer 1

[Kevin Blighe]

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