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You will need to debayer the final FITS in your post-processing software of choice. If you are using DSS (which uses dcraw), try the standard RGGB setting first - just play around until you get it right. Also in settings look at the 2nd tab to make sure you choose the mono FITS option correctly.
I assume your display/capture software does a temporary debayer for you, to give you an idea of what you are looking at.
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