FPKM = RPKM for single end reads?

[hyates]

Hi Readers,

I am a computer scientist and I am trying to understand the relationship between RPKM and FPKM. I have read this following thread and a lot of it, the biological parts, were going past me.

I ran an analysis using cufflinks/cuffdiff/cummeRbund on single ends read data. I have a cummerRbund scatter plot comparing biological condition A FMKM gene scores to biological condition B FPKM gene scores. Is this right? Or am I really comparing RPKM scores here since FPKM = RPKM when I have single reads?

If I am wrong, can someone please explain to me why they are not equivalent mathematically when given single end reads?

Thanks,
GeekyOmega

[dpryan]

Yes, FPKM==RPKM for single-end reads.

[gringer]

My understanding is that FPKM (as defined by cufflinks) approximates RPKM, but is not the same because cufflinks will distribute hits mapped to multiple transcripts across those transcripts based on the expected isoform frequencies (or possibly equally distributed).

[dpryan]

FPKM will only approximate RPKM for paired-end reads, it will be identical for single-end reads.