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My first batch is conditioning at room temp right now. I used brown bottles, but threw in a few greens and two cleat just for experimentation..... I have them in a fairly dark room but also covered them with a blanket to fully cut off all light! Good idea? Bad idea? Wast of time?

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If you have green and clear glass, then you should cover them, yes. Otherwise, if they're brown glass in a fairly dark room, I wouldn't worry about it.

If you really want to do an experiment with brown vs. green and clear bottles, then you probably do want to expose them to some light, since presumably that would be the point of the experiment.

Not quite sure what sort of answer you're after, here. :/

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I personally use an old shower-curtain, but that's just to simplify cleanup in case there's airlock blowout, or bottle bombs. – Pulsehead May 20 '11 at 13:52

I have never covered my beers and haven't had an issue with skunky beer. I do have a dark basement and have mostly covered shelves where I store all of my bottles.

As long as you keep your bottles out of direct sunlight they should be good, so if you want/need to use a blanket to help facilitate that, it's up to you. But it really is dependent on your situation.

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