Question: calculate RPKM from featureCounts result
0
gravatar for yuabrahamliu
8 months ago by
yuabrahamliu30
yuabrahamliu30 wrote:

Hi all, I have a question. I got the read counts result from some microRNA-seq bam files by featureCounts. Then, I want to transform the counts to RPKM. I think maybe the rpkm() function of edgeR is helpful. However, my question is whether I need to normalize the counts result before using the rpkm() function, or just use the counts directly? Thank you so much.

rna-seq • 606 views
ADD COMMENTlink modified 8 months ago by cindy.perscheid90 • written 8 months ago by yuabrahamliu30
3
gravatar for cindy.perscheid
8 months ago by
Hasso Plattner Institute, Potsdam, Germany
cindy.perscheid90 wrote:

Hi yuabrahamliu,

RPKM itself is the normalization function. ;) However, I would not recommend to use RPKM for your analysis, as it is considered to be not suitable anymore (see recent discussion here and publication comparing the different normalization strategies here). I would rather recommend to use DESeq2 or TMM normalization as described in the paper.

Best,

Cindy

ADD COMMENTlink written 8 months ago by cindy.perscheid90

I see. Thank you so much!

ADD REPLYlink written 8 months ago by yuabrahamliu30
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