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Understanding Join output anchors and when to add a Union tool: The Join tool anchors are separate subsets of data. You can combine them with a Union tool. The Select functionality of the Join tool applies only to the J anchor, not the R- or L-anchored data.
The Alteryx Join tool has three outputs, L, J, and R as separate subsets of your data. If you examine the output of the L (left), you will see the records that existed in the left data set, but do not match with records from the right. The J (join) output provides only the records that are common between the two data sets. And the R (right) output provides the records from the right that don't match with those on the left.
Suppose you want to change the names of the various fields or change their order. If you are using the Join tool alone to work with just the J output anchor (the Inner Join situation) you can do everything at once and use the "Select" functionality built into the Join tool. (If you are using any other anchors from the Join tool, please refer to this article for the best practices.)
You can select/deselect, reorder, rename, or change the data types and sizes of the fields using the check boxes, using the arrows at the top, and typing in the grid.
You can use the Options to reduce the number of clicks compared to manually configuring the fields.