Cuffdiff Command Line For Labels And Replicates

Question

[Johan]

I've been trying to figure out how to setup the cuffdiff command line if one wants both labels and replicates, but I think that the manual could have been more specific on this point. Should there be one label per condition of one per input file. To exemplify:

Assume that I have two conditions A and B with two samples each, then which of the below alternatives are correct?

Alternative 1: cuffdiff <other options> --labels conditionA,conditionB <annotations file> sample1.bam,sample2.bam sample3.bam,sample4.bam

Alternative 2: cuffdiff <other options> --labels conditionA,conditionA,conditionB,conditionB <annotations file> sample1.bam,sample2.bam sample3.bam,sample4.bam

Of course if I'm completely off track, please say so.

[Fabio Marroni]

I think that the labels are labels for conditions, which -at present- are two (e.g. treated and control). So, I would go for alternative 1.

[Johan]

You are right, I just finished experimenting with this myself before seeing your comment. I added it as a answer below, for future reference.

Answer 1

[Johan]

I did some experimentation of my own, and just as @Fabio Marroni suggests in his comment to my question the correct way to do it is alternative 1:

cuffdiff <other options> --labels conditionA,conditionB <annotations file> sample1.bam,sample2.bam sample3.bam,sample4.bam

[evashan96]

what is this annotation file?

[evashan96]

It is the GTF file which is merged.