I know I had a similar thread before. That one was with a .mov file made in Blender though.
This time it’s with a .mov and a .mp4 made in Shotcut.
It’s nothing too complex really:
Track 1: PNG with alpha
Track 2: PNG with alpha (S&P filter)
Export to either Quicktime or Ut Video.
That’s it!
It would be great if someone could have a look at my Shotcut file.Alpha-test.zip (77.8 KB)
Thanks in advance!
Keep in mind that both mov and mp4 are not codecs but containers.
mp4’s don’t support alpha channel.
mov does provided you export in a codec that has 4444, Pro-res or Apple Animation Codec come to mind.
It’s easy for you to check, export your video, then,
open a new SC project put something on track V1 and the newly exported clip on V2.
If it has alpha, the clip on V1 will be visible in the areas where V2 has transparency.
Thanks for replying Paul 
I had assumed that any/every choice in the alpha list would have alpha. Also, I have used Quicktime (.mov) before successfully.
I am not asking for someone to check if my video has transparency. I already know it is not rendering it.
I have checked the PNGs I am using, so I know there’s nothing wrong with them either. So it has to be the settings.
I just don’t know which setting is the problem.
Make sure you have “qtrle” selected.
From: https://en.wikipedia.org/wiki/QuickTime_Animation
QuickTime Animation format (also known as QuickTime RLE ) is a video compression format and codec created by Apple Computer to enable playback of RGB video in real time without expensive hardware.[1][2] It is generally found in the QuickTime container with the FourCC 'rle '.[note 1] It can perform either lossless or lossycompression and is one of the few video codecs that supports an alpha channel.
That comes already with the Quicktime preset and it doesn’t make a difference. I tried @Dr_Pepper_Can project with the Ut Video and Quicktime alpha presets along with one of the WebM presets and they don’t export a video that keeps the alpha channel even though his png images definitely have an alpha channel. I have to add Chroma filter to the exported videos in order to get the black background out but that defeats the whole purpose of the alpha presets.
I’ve noticed this issue before when I was testing the alpha presets in that they don’t export a video with a transparent background but I didn’t report it because I didn’t know if I was doing something wrong. In this case, I tried exporting it as @Dr_Pepper_Can has his project laid out with each png image in V1 and V2 and I also tried exporting it by adding an empty video track layer underneath the two png images as well as also exporting it with a transparent clip underneath those two. In all 3 attempts, it didn’t make a difference no matter the alpha preset. All clips came out with a solid black background.
Correct, the alpha for the resulting qtrle clip has to be told which color must become the transparency.
Not sure if it’s a SC issue or a discrepancy between alpha in png’s and qtrle.
V1 is a “standard” video clip whilst V2 is the png exported as qtrle with a Chroma filter set to black.
This issue about transparency and alpha channels has been brought up by @jonray here Can I export as a Quicktime Animation when there are multiple video tracks and maintain transparency?
When you export clips/images with alpha channels, if they are on multiple tracks the transparency isn’t preserved.
If you export each clip/image separately the alpha channel is preserved. I tested @Dr_Pepper_Cans project. Opened each image in the viewer, exported with QuickTime and webm. When the images are opened in SC the transparency is preserved.
Shout out to @jonray then. 
Sorry it was ignored before.
No problem, @drm - but thanks for your comment. My goodness, @sauron, you have a good memory! I’d nearly forgotten about that post! Thanks for the heads-up!
I notice some videos on that post have expired, but I managed to find the top video so I’ve re-uploaded it to Streamable:
https://streamable.com/snmby
Also - I recall reading a post on this from a few weeks ago about SC’s handling of transparency and I THINK it said something like this: V2, V3, V4 etc all maintain transparency when placed over V1, but you can’t maintain transparency if you put say V3 over V2 or V4 over V3 etc.
So I took it that you can’t think of tracks in SC as being multilayered, like in GIMP etc.
This is a shame because I can think of a few creative possibilities if you could be able to multilayer tracks.
I could be wrong on this, though - I’ve searched the forum I can’t find the post I was reading.
I also recall reading something about not all tracks work.
As I work around to the problem faced by @jonray where too many tracks slow down SC, I tried the following:
I created 4 simple png files with alpha, attached below.
4ClipsWithAlpha.zip (35.3 KB)
Bought those clips into SC, placed them all on the same track, next to each other, no gaps but also no overlap.
Applied a Chroma filter (black) to each one.
Now I overlapped them to create transitions.
Exported it as a qtrle mov
Attached below, it’s a real zip file, didn’t just append a .zip extension.
Alpha2.mov.zip (956.0 KB)
Bought that back into SC on V2 and my “base” video on V1.
Worked perfectly, result attached below, again real zip file.
result.mp4.zip (1.3 MB)
The idea here being to test that there are no grey transitions that @jonray mentioned in his other post and that by “down-mixing” all the overlay effects, the computer is not being so over worked.
Inspired by @Paul2’s latest post I decided to take @Dr_Pepper_Can’s project file again but this time create a new layer underneath with a color clip. I applied the Chroma Key Simple filter to the Master track head and keyed out the color clip like so:
I then exported it with the Ut Video and Quicktime alpha presets and this time they preserved the alpha channel. However, I don’t know if this is how it’s designed to work or if this is really just a workaround. I was under the impression that anything blank in the timeline is automatically an alpha channel considering that when you use single png images they preserve the transparent background no problem. So this could be a bug.
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