RPKM calculation

[adrian]

Hi:
Apologies for asking a very simple question. I could not find a reference and I had to ask here.

Mortazavi et. al - RPKM calculation

RPKM = 10^9 x C/NL

what is the significance of 10^9.

Is this the total number of bases in genome? I thought it is ~3billion bp.

thanks
Adrian

[feixue1039]

The formula to calculate RPKM (reads mapping to the genome per kilobase of transcript per million reads sequenced) should be:
RPKM=(number of mapping reads)*1000bp*1 million reads/[(length of transcript)*(number of total reads )].
Then you can find that 10^9 is correspond to 1000bp transcript multiple 1 million reads.

Hope it can help you.

feixue1039