I see. Thank you so much!
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yuabrahamliu •
calculate RPKM from featureCounts result
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.
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cindy.perscheid
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yuabrahamliu •
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yuabrahamliu •
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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
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