Yes. Truman was almost certainly referencing the case of Isaac Woodard, though Woodard was in South Carolina and hauled off a bus, not a train. But Woodard was the main catalyst for a large public outcry and reaction by Truman.

In brief: Hours after being honorably discharged, Isaac Woodard (a sergeant) was hauled off the bus he was traveling on on his way home from the army, attacked and beaten and permanently blinded by police in South Carolina. This happened on February 12, 1946.

The case gradually snowballed into getting a lot of attention, and it was presented to President Truman a few months later. Truman was furious and applied pressure to try the police--who were found to be not guilty, almost immediately. It prompted Truman to found the Civil Rights Commission in December 1946, and their recommendations led to more action on Truman's part, including desegregating the armed forces in 1948.

To piggyback this, wasn't Truman a huge racist in his private life? Why would he let the military be desegregated?