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  • questions for cuffcompare and cuffdiff output

    After I run cuffcompare, there is a prefix.loci file which is not explained in the user manual. I guess it is the combined gene file for different samples. However, after I run cuffdiff, the items in cuffdiff output genes.fpkm_tracking are much less than the items in prefix.loci. Why so many "gene" outputed by cuffcompare discarded by cuffdiff?

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