When you are setting up your analysis, click on “Change Default Options.” This will display all analysis parameters that can be changed. 

Basepair RNA-seq Expression Count pipeline using STAR

Scroll down to the section called “Trim” to view the existing default parameters and make any changes to the defaults. 

trimming defaults for Basepair's RNA-seq pipeline

As you can see from the defaults above, trimming is always on and adaptor trimming is always enabled. The default settings used in all Basepair pipelines are based on the settings recommended by the creators of the tools we use in our pipelines.