Need help for Cuffcompare Analysis

Question

[anuraj]

Dear All,

I am working on Illumina RNA-seq. I want to see the Gene Expression on both disease and normal sample. I have got TopHat and Cufflink results. I am trying to do cuffcompare and want to know how to prepare the input data for cuffcompare? I got one GTF file and 2 tabular files from cufflinks. Is it required to merge both disease and normal samples in a single tabular sheets as input for cuffcompare. it would be a great help if any one could give me an insight.

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Anuraj, [e-mail]

Answer 1

[Devon Ryan]

You don't need to merge anything for cuffcompare (just cuffdiff). Just use the GTF file produced for each of your samples, such as cuffcompare sample1.gtf sample2.gtf sample3.gtf.

[anuraj]

Thanks a lot for your suggestion.From cufflink I got 1 gtf file for disease sample and 1 gtf file for normal sample. So I should run cuffdiff separately isnt? In cuffdiff, there is a parameter to set for condition 1 and condition 2? What should be the input for condition 1 and condition 2?

[Devon Ryan]

Please read the cuffdiff documentation. They're rather clear on how this should work. Also, with just 1 control and 1 diseased sample, the output will be near-useless regardless of the tool.