Genes' length to get RPKM if features count is not used?

Question

[Sharon]

Hi everyone

We used salmon and edgeR to get expressions using cpm. Now, I need to get RPKM also, is there a way to get genes length to compute rpkm using edgeR, if I didnot use feature counts originally?

Thanks

Answer 1

[h.mon]

Salmon outputs effective gene length, and edgeR has a rpkm() function, use them to get what you want - even though you should use tpm instead.

[Sharon]

Found it, the effective length, thanks so much :)