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mattanswers started a topic Cuffdiff dilemma

in RNA Sequencing

02-17-2015, 01:17 PM
Cuffdiff dilemma

I have 4 samples, each in triplicate (A1, A2, A3; B1, B2, B3; C1, C2, C3; D1, D2, D3)

When I use Cuffdiff to compare within each...

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ae_ucla started a topic acceptable -c threshold for cuffdiff?

in RNA Sequencing

03-07-2011, 10:13 PM
acceptable -c threshold for cuffdiff?

Hi, I am using cuffdiff on single end illumina data. I naturally get a lot more significantly differentially expressed genes if I lower my threshold...

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