user9154: Is it possible to export a video file from After Effects with transparency?
I don't want to export to an image sequence.

user1871: Yes, for the Quicktime output module, choose to output RGB + Alpha using PNG or Animation codec.
In Media Encoder, choose Depth as 32 Bit after selecting the same codecs as above.

user12141: File > Add to Render Queue > Output mode > Format 'Quicktime' / Channels 'RGB + Alpha'
See if that works for you!

user6685: Production codecs with alpha channel support

Apple ProRes 4444 / Apple ProRes 4444 XQ
From the Manual: 

Apple ProRes 4444 and Apple ProRes 4444 XQ are ideal for the exchange of motion graphics media because they are virtually lossless. They are also the only Apple ProRes codecs that support alpha channels.

DNxHD 
From Wikipedia:

lossy high-definition video post-production codec engineered for multi-generation compositing with reduced storage and bandwidth requirements
The codec supports alpha channel information.

DNxHR
From Wikipedia:

lossy UHDTV post-production codec engineered for multi-generation compositing with reduced storage and bandwidth requirements

CineForm
From Wikipedia

Current implementations support image formatting for 10-bit 4:2:2 YUV, 12-bit 4:4:4 RGB and RGBA, and 12-bit CFA Bayer filter RAW compression



Uncompressed with alpha

Quicktime Animation Codec
AVI uncompressed (None)

From the After Effects Manual:

When specifying the color depth for an output image, the plus sign (as in Millions Of Colors+) denotes an alpha channel. Similarly, choosing to output to 32 bits per pixel implies an output depth of 8 bits per channel for each of four channels: RGBA.


9154: <p>Is it possible to export a video file from After Effects with transparency?</p>

<p>I don't want to export to an image sequence.</p>
 1871: <p>Yes, for the Quicktime output module, choose to output <code>RGB + Alpha</code> using PNG or Animation codec.</p>

<p>In Media Encoder, choose Depth as <code>32 Bit</code> after selecting the same codecs as above.</p>
 12141: <p>File > Add to Render Queue > Output mode > Format 'Quicktime' / Channels 'RGB + Alpha'</p>

<p>See if that works for you!</p>
 6685: <h3>Production codecs with alpha channel support</h3>

<ul>
<li><p>Apple ProRes 4444 / Apple ProRes 4444 XQ</p>

<p>From the <a href="https://support.apple.com/en-us/HT202410" rel="nofollow noreferrer">Manual</a>: </p>

<blockquote>
  <p>Apple ProRes 4444 and Apple ProRes 4444 XQ are ideal for the exchange of motion graphics media because they are virtually lossless. They are also the only Apple ProRes codecs that support alpha channels.</p>
</blockquote></li>
<li><p>DNxHD </p>

<p>From <a href="https://en.wikipedia.org/wiki/DNxHD_codec" rel="nofollow noreferrer">Wikipedia</a>:</p>

<blockquote>
  <p>lossy high-definition video post-production codec engineered for multi-generation compositing with reduced storage and bandwidth requirements</p>
  
  <p>The codec supports alpha channel information.</p>
</blockquote></li>
<li><p>DNxHR</p>

<p>From <a href="https://en.wikipedia.org/wiki/DNxHR_codec" rel="nofollow noreferrer">Wikipedia</a>:</p>

<blockquote>
  <p>lossy UHDTV post-production codec engineered for multi-generation compositing with reduced storage and bandwidth requirements</p>
</blockquote></li>
<li><p>CineForm</p>

<p>From <a href="https://en.wikipedia.org/wiki/CineForm" rel="nofollow noreferrer">Wikipedia</a></p>

<blockquote>
  <p>Current implementations support image formatting for 10-bit 4:2:2 YUV, 12-bit 4:4:4 RGB and RGBA, and 12-bit CFA Bayer filter RAW compression</p>
</blockquote></li>
</ul>

<hr>

<h3>Uncompressed with alpha</h3>

<ul>
<li>Quicktime Animation Codec</li>
<li>AVI uncompressed (None)</li>
</ul>

<p>From the After Effects <a href="https://helpx.adobe.com/after-effects/using/alpha-channels-masks-mattes.html" rel="nofollow noreferrer">Manual</a>:</p>

<blockquote>
  <p>When specifying the color depth for an output image, the plus sign (as in Millions Of Colors+) denotes an alpha channel. Similarly, choosing to output to 32 bits per pixel implies an output depth of 8 bits per channel for each of four channels: RGBA.</p>
</blockquote>
