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