Skylight leak, (I think I narrowed it down to glass seal, not roof)

During a heavy steady rainstorm yesterday, my skylight started to leak through the sheetrock. I have had issues with this in the past, but never this bad. The flashing around the skylight on the roof looks good, so I always suspected maybe its the glass and seals. During a lull in the action, I went up on the roof and put up a tarp, just covering the glass part, not the flashing.
The leak did stop, so I think I narrowed it down to the glass. So now my question is, how do I fix the seals around the glass? They do not look bad, but obviously its leaking somewhere. Would putting some clear silicon on it help?
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Might work OK, but do a bit of research with a garden hose and a helper observing to nail down the leak area first.
Joe
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