Cufflinks gene FPKM different in genes.fpkm_tracking vs isoform.fpkm_tracking

[h_manoj]

Hello,

I am worried to see different values of FPKM for the same gene in the Cufflinks genes.fpkm_tracking vs isoforms.fpkm_tracking files.

I was under the impression that one could use the genes.fpkm file if we are not worried about the isoform information. Am I wrong?

Please see example below:

login3$ grep Nox1 genes.fpkm_tracking
ENSMUSG00000031257.8 - - ENSMUSG00000031257.8 Nox1 - chrX:134086420-134221956 - - 2.56323 2.26375 2.71812 OK

login3$ grep Nox1 isoforms.fpkm_tracking |grep -v ENSMUST
ENSMUSG00000031257.8 - - ENSMUSG00000031257.8 Nox1 - chrX:134086420-134221956 135536 0.0626628 0.00383565 0.00300087 0.00468318 OK


Could someone (especially developers) please comment?

Thanks,
Manoj.