Question: Genes' length to get RPKM if features count is not used?
0
gravatar for Sharon
2.6 years ago by
Sharon490
Sharon490 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 • 569 views
ADD COMMENTlink modified 2.6 years ago by h.mon31k • written 2.6 years ago by Sharon490
2
gravatar for h.mon
2.6 years ago by
h.mon31k
Brazil
h.mon31k 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 2.6 years ago by h.mon31k

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

ADD REPLYlink written 2.6 years ago by Sharon490
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