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Hi Markus,
Yes, you'll need to do a batch debayer as the very first step, before anything else. You could check your matrix choice using the script at:
Script/Batch Processing/Batch DeBayer
Once you're getting proper RGB files, the best option to probably just use the Batch PreProcessing script - which will debay, calibrate, stack etc for you - then you can concentrate on processing your stacked master image.
(note: the real gurus play with the final stacking settings to optimize signal to noise, but the defaults usually work well, especially while you're learning)
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