Question: RUnning cuffdiff on 2 conditions w/ no replicates
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gravatar for onspotproductions
21 months ago by
United States
onspotproductions40 wrote:

I have two sets of data; 12 hours control and experiment and 48 hours control and experiment. I am only interested in known transcripts so I will be using cuffdiff directly. My question is how do I properly combine the controls and each time period as replicate groups in cuffdiff? Do I create a group for each time period and just add the control and experiment in batch mode, or do I add the control and experiment as individual replicates in each group?

rna-seq cufflinks expression • 721 views
ADD COMMENTlink modified 21 months ago by Jennifer Hillman Jackson23k • written 21 months ago by onspotproductions40
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gravatar for Jennifer Hillman Jackson
21 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Replicates are not the same as treatment/control bundles. All replicates under the same conditions should be similar datasets (e.g. treatment).

Cuffdiff only provides a complete comparison of two conditions when used in Galaxy. Perhaps run the tool through with conditions as treament and control (twice, one for each time-point), then run the two conditions as treatment only (no controls). Then compare the final results, using the treatment-control runs to normalize the treatment-only results.

Others here may have alternate advice. For example, Cuffnorm could be useful. See the manual for how/when to best employ in an analysis. http://cole-trapnell-lab.github.io/cufflinks/manual/

Jen, Galaxy team

ADD COMMENTlink written 21 months ago by Jennifer Hillman Jackson23k
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