There was a hot discussion that RPKM should not be used in the RNA-seq analysis:
blahah404 Woohoo - death to FPKM and RPKM!t.co/CyR3ht1dqi
However @BioMickWatson has a different opinion, he thinks FPKM makes sense.
Why FPKM makes sense
what is RPKM or FPKM? see blog posts below:
update on 07/23/2015, see a youtube video for great explanation of the three.
What is the FPKM? A review of RNA-Seq expression units
Counts vs. FPKMs in RNA-seq
Paper: RPKM measure is inconsistent among samples
FPKM/RPKM normalization caveat and upper quartile normalization
Finally a post from Lior Pachter
Estimating number of transcripts from RNA-Seq measurements (and why I believe in paywall)
I personally use raw counts and let DESeq2 to deal with normalization.
update on 07/08/2016.
Salmon and Kallisto outputs TPM, but if you want to convert counts to TPM, read this biostar post, and my post comparing salmon, kallisto and HTseq.
This blog by Tommy Tang is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
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