Identifying root cause of slow query outliers from pt-query-digest?

I've run pt-query-digest and noticed many outliers with very high query times. Many of these queries do not perform slowly when I run them myself, and I'm having trouble figuring out the root cause of these sporadic slow queries. Is there another tool I might use to shed more light on this situation? What might cause the same query to only be slow *some* of the time?