Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: Genes' length to get RPKM if features count is not used?
0
gravatar for Sharon
2.8 years ago by
Sharon • 510
Sharon • 510 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 COMMENT • link •
modified 2.8 years ago by h.mon ♦ 32k • written 2.8 years ago by Sharon • 510
2
gravatar for h.mon
2.8 years ago by
h.mon ♦ 32k
Brazil
h.mon ♦ 32k 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 2.8 years ago by h.mon ♦ 32k

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

ADD REPLY • link written 2.8 years ago by Sharon • 510
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1727 users visited in the last hour
_