To transform your data you don't need to load all of it into hale»studio. Usually it's a better practice to only load a representative sample of your data, to help you verify the mapping and quickly get feedback on its transformation. Once you have defined the mapping you have the possibility to transform your data without loading it into the project, but launching a dedicated data transformation job.
To 
transform external data, select
Transformation→Transform external data... from the main menu.
Next you will be prompted to select source data files that you want to use.
Click on Add source file to add another file.
The instance import wizard will open for you to select the file of your choice.
After adding at least one file you can proceed to select the target file as in the
transformed data export wizard.
If your alignment only contains one-to-one type relations, e.g. Retype,
the data will directly be transformed and streamed from the data source to the target file.
If you also use for example Merge or Join the source
data will first be read into a temporary database for performance
reasons.
Working with a source data set
For information on the import wizard.
Save the transformation result
For information on the export wizard.