Generally, guys should feel fairly safe in Japan.
For the girls, be careful of taking the crowded commuter trains between 7am-9am and 6pm-11pm. It is a known fact that there are gropers (sukebe) who like to molest foreign females and go undetected in crowded trains.
Also beware of what I call the 'Ruthies' - basically 60+ year old Japanese women who will do anything to get that seat. Be prepared to be pushed aside. Grin and bear it.
Public toilets at the train stations can be a little basic. They are generally the squat type - make sure you face towards the jet and flush only once you have moved away to avoid being 'splattered'. Always carry your own little supply of tissues as none are generally provided.
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