Question: Genes' length to get RPKM if features count is not used?
0
gravatar for Sharon
2.8 years ago by
Sharon510
Sharon510 wrote:

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

edger rna-seq salmon rpkm • 604 views
ADD COMMENTlink modified 2.8 years ago by h.mon32k • written 2.8 years ago by Sharon510
2
gravatar for h.mon
2.8 years ago by
h.mon32k
Brazil
h.mon32k wrote:

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.

ADD COMMENTlink written 2.8 years ago by h.mon32k

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

ADD REPLYlink written 2.8 years ago by Sharon510
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