First, you need to select a media container and codec that support alpha channels. The three I'm certain will work are all quicktime movies, in the Animation, PNG or ProRes 4444 codecs. You may have to create a custom preset for them in AME. DNxHD is also supposed to support alpha channels, but I'm uncertain of its status in certain versions of AE.
There are more, but others will have to tell you about them.
wow Thanks for the quick response. I have no problems getting an RGB+Alpha Tiff sequence directly out of After Effects. I would really like to use the Command File>Export>Add to Adobe Media Encoder Queue. . . But unlike the After Effects Output Module Settings of the Render Queue I find no option in the Media Encoder to define output as RGB+Alpha or to define the Alpha as Premultiplied or Straight. Even if I try to create a new Preset in Media Encoder.
Therefore I kind of think this isn't actually possible but is what I need at the moment.
It's been more than a year and a half since I set up my Alpha Channel Quicktime Movie settings in AME, and guess what? I'm nowhere near my machine to retrace my steps, so I can't telll you how to do it.
Suffice it to say it CAN be done, but it doesn't work the same way as the AE Render Queue. Imagine that.
sorry about this dave but It does actually seem to do what I want after all. Still I don't get any choices in Encoder to define straight or premultiplied Alpha channel, so I presume it looks at the output module which I have set in After effects as the default export Module?? any thoughts??
Yes: search further in those settings. As I recall, getting to the straight/premultiplied selection takes you to a very Quicktimey-looking window.
You want STRAIGHT alpha in almost every case. Avid, FCP, PPro, AE and every other compositing or editing app I've ever used prefer straight alphas.
Create a custom template using, for example, QuickTime JPEG2000 and pick 32Bit like this.
You'll end up with a straight alpha QT that will work just fine in any app. If you must have pre-multiplied then you have to use the Render Cue and beware of the edges when compositing.
Here's the result of the test render in AE. Note the file interpretation and the transparency.
BTW, you can save the preset (I did) and use it at any time by adjusting AME's preferences.
A big thanks to Rick and Dave for the very fast answers