1) Send your troops to a jagged line of coast.
2) Send a transport ship to the same place
3) Right click the transport ship you send and click Embark
4) Hover over the troops and wait until the symbol changes and click
5) Once the troops are embarked, move the ship to where you want them to be disembarked.
6) Right click the ship again and click Disembark.

I would point out it's not wise to do this because troops will just instantly die when they get scared, so always try to give protection to each side of the Nile.