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burt 08-23-2011 11:59 PM

Cufflinks' computation of FPKM for --GTF and --GTF-guide estimation

I was wondering if someone in the community would be able to shed some light on how Cufflinks compute the FPKM values when run under the --GTF and --GTF-guide modes.

From my understanding of FPKM, the denominator would be the number of fragments mapped in the input data (in millions). This would be easy enough to understand when running Cufflinks in the --GTF-guide mode.

But what would this denominator be when we run Cufflinks strictly focusing on known genes using the --GTF mode? Would this denominator change to the number of reads that mapped to the regions specified in the GTF (in millions)?

Hoping to get some insight from the community.

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