Most of the advice for setting up an allergen proof room calls for the the removal of all carpeting and rugs.  The reason for this advice is that it is impossible to really get carpet clean. Carpet companies hate it when I say that.

The carpets on our floors are a perfect environment for collecting dust mites and other common household allergens.  Dust, pollen, dirt, crumbs, and other debris fall onto the floor and are caught in the fibers of the carpet.

Since dust mites feed on shed human skin (a major component of household dust) carpeting provides an absolute banquet table set for a feast for dust mites.  As we walk on the carpet, we stir up the settled bits of allergen, causing them to become air-borne.  Once air-borne, they are easily inhaled and can trigger an allergic reaction.

Now you can pay a company to come clean the carpets and rugs but the most effective way is to get rid of them all together. The truth is that is not an option for most people.

Here is some information from the Allergy Store on a product called Allersearch X-Mite Carpet treatment. People who suffer from allergies have been using it for years.