The direction of your flooring will all depend on the layout of your home. It is not a great idea to change the direction of hardwood flooring from room to room because it causes a safety issue and also breaks up the harmony within your home. Otherwise, the hardwood flooring planks will fall in at some point due to the floor being unstable.
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You should install your hardwood flooring to be perpendicular to the joists.
Because you need the flooring planks to be perpendicular to the joists, you have to work with them.