To have natural scroll for ubuntu that applied to system wide, do the following command on terminal:

sudo nano /usr/share/X11/xorg.conf.d/20-natural-scrolling.conf

Then in the editor copy (ctrl+c) and paste (ctrl+shift+v) below:

Section “InputClass”
     Identifier “natural scrolling for mouse wheel”
    MatchIsPointer “on”
    MatchDevicePath “/dev/input/event*”
    Driver “mouse”
    Option “Device” “/dev/input/mice”
    Option “Protocol” “Auto”
    Option “ZAxisMapping” “5 4”
EndSection

Save (ctrl + 0) and Exit (ctrl+x)

Reboot (sudo reboot)

After reboot, now you have natural scroll in your ubuntu system