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Question: Genes' length to get RPKM if features count is not used?
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gravatar for Sharon
2.6 years ago by
Sharon • 490
Sharon • 490 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
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modified 2.6 years ago by h.mon ♦ 31k • written 2.6 years ago by Sharon • 490
2
gravatar for h.mon
2.6 years ago by
h.mon ♦ 31k
Brazil
h.mon ♦ 31k 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 COMMENT • link written 2.6 years ago by h.mon ♦ 31k

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

ADD REPLY • link written 2.6 years ago by Sharon • 490
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