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


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