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Cuffdiff Command Line For Labels And Replicates

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.

cuffdiff
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written by Johan Johan

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.

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written by Fabio Marroni Fabio Marroni

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

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written by Johan Johan

1 answer

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

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written by Johan Johan

@JohanI want to run cuffdiff for groups. do you think the below command works?

cuffdiff -o diff_out4 -b ../genome/ce10.fa -p 2 -L SRR493359,SRR493360,SRR493361,SRR493363,SRR493364,SRR493365 -u merged_asm/merged.gtf ../tophat/em/SRR493359_thout/accepted_hits.bam, ../tophat/em/SRR493360_thout/accepted_hits.bam, ../tophat/em/SRR493361_thout/accepted_hits.bam ../tophat/la/SRR493363_thout/accepted_hits.bam, ../tophat/la/SRR493364_thout/accepted_hits.bam, ../tophat/la/SRR493365_thout/accepted_hits.bam

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written by Vasu Vasu

It is the GTF file which is merged.

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written by evashan96 • evashan96

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