cufflinks -G vs cuffquant

[spaceace507]

I have a collection of bam files and a reference transcriptome (.gtf), and I want to generate expression levels that will be correlated with a phenotype.

cufflinks -G .gtf .bam will generate fpkm values for transcripts and genes.

cuffquant .gtf .bam -> .cxb
cuffnorm .gtf *.cxb will also generate fpkm values, as well as "normalized" expression values
(too many bam files to store and run together, the .cxb files are much smaller)

Is there a difference between the fpkm values from cufflinks -G vs cuffquant->cuffnorm?

fpkm is a type of normalization. Can anyone explain the additional normalization provided by cuffquant->cuffnorm?

Thanks in advance for any comments.