That topology wont work for getting HV for driving a nixie tube. The 
original design uses an inductor and operates as a boost-converter to 
produce a higher output voltage, generally around 5V, from the input.

When you replace the inductor with a transformer, you are taking energy out 
of the circuit and it changes the operation radically. I'm sure you will 
see a strange-looking waveform at the secondary of the transformer on a 
scope, but it most certainly wont be a DC voltage. Even if you use a half 
or full-wave rectifier + filter, you wont have enough energy to drive a 
nixie.

I suggest you look at a flyback converter, and study the underlying theory 
carefully, and run SPICE simulations on the design. I usually spend several 
months simulating a flyback converter just to get the design working, and 
spend even more time debugging the real hardware.

Be very careful about the transformer selection, especially it's saturation 
current for the primary winding.

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