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Old 05-11-2012, 05:27 AM   #1
Dbuch
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Default 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 at 10:41 AM.
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Old 07-17-2012, 10:45 AM   #2
muehlsch
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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 ?
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Old 05-22-2014, 07:20 PM   #3
vramnarine
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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
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cuffdiff, cufflinks, frag-bias-correct, min-alignment-count, rna-seq

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