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Animation Codec will work just fine. In most cases you want to render straight alpha. Just set up the output module as shown.
You should also check the Help files and look for Rendering and Exporting.
Animation Codec set to best with Millions of Colors+ (+ gives the alpha information)
If you don´t have any transparency (e.g. because of a color Solid behind) in your comp then there will be no Alpha information when rendering out.
be aware that the animation codec does not work well in the FCP timeline and has to be rendered any time changes have been made.
EDIT: Thanks Rick!
I can see I just missed the pulldown for the Channels options! Oddly in FCP it has 3 settings for Alpha channel, straight, black, white. I thought an Alpha channel was just that never had options before!
Anyway, all working now so many thanks.
There are 2 types of Alpha channels - Straight and Premultiplied. In order to import the alpha into PS and Avid (and possibly other apps), you need to render it as Straight.
The other FCP options (white, black) refer to premultiplied alphas - depending on if the bg color is black or white.
Another thing with Alphas, if you see a halo (white glow) around your object, 99% chance that you set the alpha to straight as opposed to premultiplied.
Thanks that is all very enlightening :-)