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I'm joining data from PostGIS and SpatiaLite databases in QGIS using the "Join attributes by location" (Vector -> Data management Tools) tool. However, this has a big limitation - I can only save the result as SHP files, which truncates my column names because of the 8 character limit. Is there any way to save to a different Format, or can I go another way (maybe a spatial join on the SpatiaLite database)?

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Go to Processing -> Toolbox -> QGIS geoalgorithms -> Vector general tools -> Join attributes by location (if you don't see this algorithm, you might need to activate the "advanced interface" option at the bottom of the Processing Toolbox dock widget).

This way you can save your results to several formats, including .sqlite.

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