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Question: q values p values from Cuffdiff are same for different samples
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gravatar for brainaneurysm1
2.2 years ago by
brainaneurysm1 • 0
brainaneurysm1 • 0 wrote:

I ran some human samples for mapping with BWA, Cufflinks, and Cuffdiff. When I looked at significantly regulated genes, q values p values from Cuffdiff are same for different samples. Does anyone have the same problem?

Thanks in advance
interpreting-results output rna-seq qa input • 756 views
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modified 2.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.2 years ago by brainaneurysm1 • 0
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gravatar for Jennifer Hillman Jackson
2.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Two different experiments produced the exact same values (assuming you are comparing by gene_name identifier)? This sounds like a data mixup. Are you certain the original sample inputs were not the same content? I can't think if any other way you would have the exact same values for two distinct complete runs (even replicates will have some variation).

Jen, Galaxy team
ADD COMMENT • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k
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