Question: RUnning Cuffdiff on 2 conditions simultaneously
gravatar for onspotproductions
4.8 years ago by
United States
onspotproductions140 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?

In addition, If I have a sample with two replicates and a control with two replicates do I add both controls and both experimental replicates to individual groups?

ADD COMMENTlink modified 4.8 years ago by Benn8.0k • written 4.8 years ago by onspotproductions140
gravatar for Benn
4.8 years ago by
Benn8.0k wrote:

For your first question, according to the manual (, cuffdiff compares all samples pairwise. So choose afterwards what relevant contrast you want to have. There is btw also a time series option.

I do not exactly understand your second question, can you be more specific about what you mean by replicate? Do you mean technical replicate?

ADD COMMENTlink written 4.8 years ago by Benn8.0k

The second question I figured out. With the time series I am still a little confused. So I would put in the command line 12 hours.bam \ control1.bam \ 48hours.bam \ control2.bam and it would compare each to the control. I am not looking to compare expression between two time points, but would like to have some indication that the log2 values it produces are correct since for this sample I do not have any technical replicates.

ADD REPLYlink written 4.8 years ago by onspotproductions140
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