This works:
Y = [-3,-2;2,1;1,-1;4,3;-1,4];
hb = bar(Y);
hbc = get(hb, 'Children');
set(hbc{1}, 'FaceColor', 'r') % Red bars for first column
set(hbc{2}, 'FaceColor', 'g') % Green bars for first column
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