Cufflinks or Cuffdiff for frag-bias-correct?

[Dbuch]

Both Cufflinks and Cuffdiff have a frag-bias-correct option (-b). Does it matter at which step I use this option or if I use it at both steps?

Same question for -u/--multi-read-correct

Thanks!

[muehlsch]

I am also very interested in the answer. At present, when I run cufflinks with bias correction, the program run terminates with an d error. However, when I use cuffdiff with bias correction on the cufflinks runs without bias correction, they work just fine.

So, is it sufficient to bias correct in cuffdiff rather than cufflinks ?

[vramnarine]

Have either of you found an answer to this question?

Ive posted a similar thread here:

http://seqanswers.com/forums/showthread.php?t=43523

No response yet.

The parameters seem redundant and Im unsure why you would need to set them for cuffquant (new workflow) and/or cuffdiff