I have two shapefiles that partially overlap. One (the bigger one) consists of several polygons which represent fields I am interested in. The second, is a rectangular shape that overlaps about 30% of my first shapefile and hold information about soil texture. I want to clip my first shapefile to the extends of the second and then find out the soil texture for each of the polygons of the first shape. I tried the merge function and the intersect function in Qgis so far. The merge seemed to be a shapefile consisting only of information of the soil texture but I could not find my fields in it. The intersection gave me an empty shapefile. Can someone point me in the right direction by providing some procedure names (preferably in R) two achieve what I need. I think I am searching with the wrong keywords here but as a newbie that is what happens;)
I think you are looking for the Intersection tool available in QGIS.
In the following picture each feature of the blue polygon has a soil attribute and while the red polygon is the polygon of your clip.
Using the Intersection tool in QGIS (Vector -> Geoprocessing -> Intersection) or in Processing (open the Processing toolbox and type Intersection) the green layer is the resulting one:
Notice that the attribute table of the green layer is made up by each matching field of the intersection layers.
Hope this helps!