I have to choose how to render a project from Kdenlive, what is the best format for Peertube? Something like .mp4/.mkv?
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On most instances it gets re-encoded anyways.
Your best bet is probably WebM with H264 video.
If you are looking forward AV1 is probably the best option but many current devices are still lacking hardware decoding. H265 is very widely supported for hardware decoding but some browsers don’t support it.