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Horizontal jigs work great for "shaking" techniqes, dead sticking a minnow, or slow lifting. Vert. jigs work great when fish are hitting jigs on the fall, because they will lay on there side an flutter when you let them fall on a slack line. Both have there place.
i use horizontals 90% of the time. they work best when rod tapping and jiggling. just make sure to tie direct with palomar knot and keep knot centered and on top of eye to keep it hanging level.