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Here's an example:

Once you've run the program you can use it to play the tones.

OR

Once you've run the program, you can use it to play the tones.

Should I use a comma where I used it or not?

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The important fact is that the first part is an adverbial clause. This means a comma works well. I wouldn't go so far as to say it was wrong without it, but it seems to read with a more natural rhythm if you use the comma.

If you had said "You run the program and then you use it to play the tones.", there is no adverbial clause (they are independent clauses); I would not say it needs a comma. But some people would prefer a comma in that sentence as well.

I don't think you're quite ready for the "when in doubt, take it out" rule, because you are so often in doubt. And, indeed, there are many subtleties to consider, few hard-and-fast rules, widely varying opinions, and an ongoing evolution in style. I suggest, if you don't already have one, get a copy of The Elements of Style by Strunk & White. That book is now considered quite traditional, but after you absorb their advice, you can begin to develop your own judgment as to when to "take it out".

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