Export with alpha?

[Colin Braley]

Bring it into AE, do whatever you need to do with it, add it to the render queue. Then click on the text next to thw words “output module.” Change the format to any type of image sequence such as Tiff of Targa. Just make sure under channels it says “RGB + Alpha.” Also, depth has to say something like “Millions of colors +” or “Trillions of Colors +.” The plus sign indicates that an alpha channel can be exported. Also, keep in mind that you can add extra output modules to do things like exporting the RBG channels separate form the alpha.
~Colin

[Adolfo Rozenfeld]

The Animation codec (Quicktime) and Uncompressed (AVI) are two standard codecs that support embeded alpha channels in a video file, avoiding the cumbersome experience of exporting and later managing still image sequences. Both can be set to RGB+Alpha, as Colin explained.