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  • cufflinks -G vs cuffquant

    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.

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