In our set of tools there exist two sorts of empty cells:

Cells without any content. These are empty strings and do not even contain white space. In a tab separated file an empty cell is simply a tab character followed by another tab character, \t\t.
Due to limitations in software processing tab-separated files, we have introduced a special string for empty cells, –. Therefore, no cell generated by our tools will contain an empty string. See the –empty-cell option in common command line options for further information.