If you need to sneeze or scratch an itch during meditation, you should go ahead and take care of it. It may be more of a distraction if you are actively trying to ignore it. You may find that, over time, you are more able to ignore something like a sneeze or an itch without even trying.
Similarly, if you try to ignore an urge to use the bathroom you may find it really difficult to meditate. In this case you should stop meditating, take care of your business, and try to pick up where you left off, or start over if necessary.
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