It's the first time for me to use cufflinks in galaxy, two choices confused me as follows:

Perform Bias Correction:

Bias detection and correction can significantly improve accuracy of transcript abundance estimates.

Set Parameters for Paired-end Reads? (not recommended):

what is the Bias correction and how does it work? And for "set parameters for paired-end reads? (not recommended)" ,what would be important difference between recommended and not recommended?

Thanks a lot!

dongdong