a question about rpkm calculation

[camelbbs]

Hi
I want to ask an important question in RNAseq:

why I need to include the reads in intron while i calculate the RPKM for one gene or transcript/isoform.

I think it is necessary to exclude the intronic reads because we only focus the mRNA expression level. (Here gene level means the mRNA).

I've discussed this queation with some forums but can't get a satisfied result.

thanks!!

[Torst]

You should not have any reads in your introns if your data is RNA ?

[camelbbs]

i don't know. But RNAseq will also give many reads at annotated intron regions, right?