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Old 07-01-2010, 11:42 AM   #1
jebe
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Location: New Mexico

Join Date: Nov 2009
Posts: 9
Default Strange cuffdiff result (disagreement between tracking and diff files)

I ran cuffdiff specifying the ensembl gtf across 4 mRNA-seq samples. The output from 0_1_gene_exp.diff for gene GNAS is as follows:

ENSG00000087460 GNAS chr20:56848167-56919644 NOTEST 0 0 0 1 0 no
ENSG00000213705 GNAS chr20:56848167-56919644 NOTEST 0 0 0 1 0 no

However, the genes.fpkm_tracking file give the following values:
ENSG00000087460 - - GNAS - chr20:56848167-56919644 419.355 412.28 426.43 449.217 449.217 449.217 384.583 374.229394.936 359.828 352.604 367.052
ENSG00000213705 - - GNAS - chr20:56848167-56919644 1.48557 1.48523 1.48592 0 0 1.23606e-156 7.94273e-05 7.94251e-05 7.94296e-05 5.62865e-10 5.62865e-10 5.62865e-10

For ID ENSG00000087460 there is disagreement between the numbers in the 2 files. Does anyone know why this might be? I discovered this when looking at wiggle plots created based on the SAM file (for sample 0) that is the input to cuffdiff. Thank you!
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