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If a chromatographic column is not placed in a vertical position, the flow and the separation rate of the materials which are been separated may be negatively affected, that is, it may  be slowed down, this is because the column is not inclined in the same direction as the flow of the separating substances. Also, collecting the products of the separation will be a bit difficult. If the column is placed in a vertical position, then a test tube can be placed at the end of the column for collecting the separated product
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Universidad de Mexico