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This question already has an answer here:

I'm trying to count points within a polygon but it's not working.

I think it has something to do with the co-ordinate system.

The points are from a text file and the line are from a dxf file. I had to set the co-ordinates for both as one was lat long and the other was an old Irish grid co-ordinate system.

When I buffered and dissolve the lines the resulting layer defaulted to the original co-ordinates.

I reset the line file to the correct co-ordinates and ran the query to count points within a polygon. The resulting layer defaulted to its original co-ordinates and all the values were null.

marked as duplicate by underdark qgis Aug 20 '18 at 16:13

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For doing a spatial query (what points in polygons is) you better have all layers and project in the same CRS.

I suggest you reproject the layer with lat lon to that old irisch CRS (or visa versa).

You can do that by choosing save as (right-click on the layer in the layerspanel). There you can define your new crs:

enter image description here

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