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  • Cuffmerge related query

    I have a query regarding what samples should be merged using cuffmerge, when you have multiple phenotypes (each with replicates). Lets say my mouse dataset comprises of one set of RNA-seq samples resulting from mutation of gene X, while there is another set resulting from mutation of gene Y. So the samples are:

    Samples:
    GeneXmutation (3 reps)
    GeneYmutation (3 reps)
    B6ctrl (3 reps)
    MixedCtrl (3 reps)

    The cuffdiff comparisons of interest are:

    Phenotype A: GeneXmutation (3 reps) vs B6ctrl (3 reps)......[GeneX mutation is on the B6 background]
    Phenotype B: GeneYmutation (3 reps) vs MixedCtrl (3 reps)....[GeneY mutation is on the Mixed background]

    I have the cufflinks assemblies for each of the 12 samples. My question is: should the cufflinks assemblies (transcripts.gtf) of all the samples above be merged one time using cuffmerge (all 12 samples as above) OR I should be running two cuffmerges: one for Phenotype A comparison and other for Phenotype B comparison? Does one approach over the another make a huge difference?

    Thanks

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