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Old 12-19-2011, 06:19 AM   #1
Location: Italy

Join Date: Feb 2011
Posts: 16
Default difference fpkm_tracking file

Hi all,
I have a question about difference between fpkm_tracking file from cufflinks quantification and cuffdiff differential expression.
I don't understand why the same gene in genes.fpkm_tracking file from cufflinks quantification and cuffdiff approach has different fpkm values.
I have replicates and I know that cufflinks assignes specific fpkm file for each replicate while Cuffdiff joins the results in a single values for all replicates but if I do the average of the replicates the results are very different.
An example
XLOC_007321 0 11.9887 36.8256 0 32.2325 cuffdiff
XLOC_007321 0 0.751042 0.730162 0 5.822425 cuffdiff

please answer me!!!
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