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