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Question: Genes' length to get RPKM if features count is not used?
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gravatar for Sharon
19 months ago by
Sharon • 460
Sharon • 460 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 • 428 views
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modified 19 months ago by h.mon ♦ 28k • written 19 months ago by Sharon • 460
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gravatar for h.mon
19 months ago by
h.mon ♦ 28k
Brazil
h.mon ♦ 28k 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 19 months ago by h.mon ♦ 28k

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

ADD REPLY • link written 19 months ago by Sharon • 460
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