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Hi Duncan so I don't confuse the issue, here's a generic flow that you can refine - should be a good starting point for you:
1_ Take 40 flats at 9000ADU and stack them into one master.
2_ Take 40 bias and stack them into one master.
3_ Calibrate all your light frames (subs)
4_ Save them into a "calibrated" directory
5_ Debayer all your subs into a Red, Green & Blue directory (separate channels)
6_ Select the best sub in each channel to register to and align.
7_ Do your data rejection, stack to mean. Build the three color masters (save as FITS).
8_ Create you color by combining the masters (save as FITS).
9_ DDP/Deconv then save as a scaled TIFF.
10_ Season to taste in Photoshop.
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