Yes. You generally run a siphon from the primary, and keep it off the bottom. Many people use a racking cane, which also includes an additional cap on the bottom which acts as a bit of a filter if you get too close to the bottom.
You also want to avoid splashing when transferring to the secondary as you don't want to introduce any oxygen at this point. This is most easily accomplished by making sure your siphon hose extends to the bottom of the secondary.
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