Dear All, I am looking for the differential splicing events between cell types. Although I got a lot of helps from Jen and from protocols found online, I am still not sure about some settings for Cufflink, Cuffmerge and Cuffdiff. 1) For Cufflink: There is a setting for Bias Correction. I made the setting as below: Perform Bias Correction: Yes Reference sequence data: Locally cached Did I make the right settings? 2) For Cuffmerge: As for whether use sequence data, I made the setting as below: Use Sequence Data: Yes Choose the source for the reference list: Locally cached Did I make the right settings? 3) For Cuffdiff: There is another choice whether perform Bias Correction, I made the setting as below: Perform Bias Correction: Yes Reference sequence data: Locally cached Did I make the right settings? Thanks. Jianguang