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I've had success marking any URL with /shorts/ in it as read. I use FreshRSS and its URL matching is pretty reliable.
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I see people are doing scripts or other things to remove shorts from their feeds, but there is a simpler solution. Take your RSS URL of a channel, e.g.:

https://www.youtube.com/feeds/videos.xml?channel_id=UCxSGC9B...

Replace the `channel_id` with `playlist_id` and replace `UC` with `UULF`. This prefix will only list normal videos:

https://www.youtube.com/feeds/videos.xml?playlist_id=UULFxSG...

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From this comment: https://news.ycombinator.com/item?id=48032508

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I went to see a video I'd uploaded to Youtube a while ago and it's now a short. I have no idea how it became a youtube short. Either I grandpa'd it or they upgrade all vertical form video to shorts.

https://www.youtube.com/shorts/qc5PKbJ3tq4

Entirely possible it's the former.

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They have been “upgrading” old videos to shorts for more than a year. As far as I know it once started with videos with a runtime of at most 30 seconds. At some point that was increased to 3 minutes. I think they do this to square and portrait videos, maybe the check is as simple as “height >= width and duration <= 3 minutes”?
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Out of curiosity, are you filtering out shorts because of YouTube's terrible Shorts UI, or solely because of shorts' content quality?
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Most channels post just clips of full videos on Shorts, it's not original content.

I've already seen the full video, I don't want to see clips of it again.

Also 90% of my RSS reading is done on a desktop/laptop and it feels "wrong" to watch 30 second vertical shorts on a 32" display :D

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Not OP, but because IMO shorts are mentally harmful. They're the mental equivalent of transfats-heavy foods.
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