By deleting a transaction from the record, you will also delete it from the register. If you prefer to delete it going through the register, instructions can be found here.
Find the individual or organization record that this transaction is in.
On the right-hand side of the record, find the Financials area.
Click on the Details button.
Find the transaction you wish to delete and click Modify.
A split screen will come up with the transaction screen on the right-hand side. Click on the Delete button.
You will be asked to confirm the deletion.