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Dbuch 05-11-2012 05:27 AM

Cufflinks or Cuffdiff for frag-bias-correct?
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


muehlsch 07-17-2012 10:45 AM

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 05-22-2014 07:20 PM

Have either of you found an answer to this question?

Ive posted a similar thread here:

No response yet.

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

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