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I've just used the readCufflinks() function in CummeRbund to create a CuffSet instance from Cuffdiff output, but it seems there are genes and isoforms missing.
In the assembly I supplied to Cuffdiff (which I produced using Cufflinks and Cuffmerge), there are 40,568 genes and 67,586 isoforms, but the CuffSet instance has only 40,567 genes and 67,454 isoforms. Does anyone know the reason for this discrepancy?
In the assembly I supplied to Cuffdiff (which I produced using Cufflinks and Cuffmerge), there are 40,568 genes and 67,586 isoforms, but the CuffSet instance has only 40,567 genes and 67,454 isoforms. Does anyone know the reason for this discrepancy?