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I want to do something like below:

DELETE UserPredictions
  GROUP BY UserId
  HAVING COUNT(*) < 500

But I'm getting a syntax error. Is it even possible to do a delete with a HAVING clause in SQL Server or will I have to roll the counts up into a CTE and do a delete with a join?

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Not really. The having clause implies an aggregation, which means you don't have the original rows any more.

I think you want the following:

DELETE from UserPredictions
where UserId in (select UserId from UserPredictions group by UserId having count(*) < 500)

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