[Bakterien]

Trying to optimize a diastereoselective reaction. It's not a double bond, it's substituted cyclohexane. Anyway, when performing a GC on the crude I get 2 nice peaks with correct mass (80:20). The separation was good but when I did the analysis again with a diffrent GC method (same sample) the cis/trans ratio changed to (65:35). Whats wrong? Epimerisation?

How do I calculate the correct ratio? Do I need to performe NMR  ?

[AlphaScent]

NMR is going to be much more definitive.  Can you show the structures? 

Your issue with NMR may be overlapping shifts, but various NMR solvents can help to spread apart some of the overlap.  Even more so if you have a 600 or 800 MHz NMR at your disposal.  What strength magnet do you have access to?