Question: calculate RPKM from featureCounts result
0
gravatar for yuabrahamliu
4 days ago by
yuabrahamliu10
yuabrahamliu10 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 • 101 views
ADD COMMENTlink modified 4 days ago by cindy.perscheid80 • written 4 days ago by yuabrahamliu10
3
gravatar for cindy.perscheid
4 days ago by
Hasso Plattner Institute, Potsdam, Germany
cindy.perscheid80 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 4 days ago by cindy.perscheid80

I see. Thank you so much!

ADD REPLYlink written 4 days ago by yuabrahamliu10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1488 users visited in the last hour