15 Mar
2013
15 Mar
'13
11:10 a.m.
The header of the Cuffdiff tool page says it is version 0.0.5
This version is the Galaxy tool wrapper version, not the tool version. (Yes, this is a usability issue.) You can find the tool version in the dataset's information panel by clicking on the 'i' icon.
Is there a way, or setting, on Cuffdiff 2.0 to revert the parameters to be more similar to Cuffdiff 1.3?
This isn't a parameter issue. The Cuffdiff algorithm has changed substantially, and it's not clear to me if/how (or whether it's a good idea at all) to modify parameters to obtain 1.3-esque results. Best, J.