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  • 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

    Thanks!
    Last edited by Dbuch; 05-11-2012, 10:41 AM.

  • #2
    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 ?

    Comment


    • #3
      Have either of you found an answer to this question?

      Ive posted a similar thread here:
      Application of sequencing to RNA analysis (RNA-Seq, whole transcriptome, SAGE, expression analysis, novel organism mining, splice variants)


      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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