Question: which file and column outputted from Cuffdiff corresponds to each sample FPKM standard deviation?
gravatar for yff
4 months ago by
yff0 wrote:

Hello everyone.

I am using cuffdiff command from cufflinks pipeline to find the genes that are differentially expressed between case and control samples. I have got several files outputted from cuffdiff. I would like to have the standard deviation of FPKM values of samples. I am not sure which file and column I should be looking at. I checked the gene_diff.exp file but I cannot find the information about standard deviation of FPKM values.

Does anyone know how can I get this information?


rna-seq sd cufflinks fpkm cuffdiff • 217 views
ADD COMMENTlink written 4 months ago by yff0

Why are you using CuffDiff? - one should now be using the upgrades to TopHat + Cufflinks, i.e., HISAT2 + StringTie. Also, FPKM expression units are not suitable for differential expression comparisons.

ADD REPLYlink written 4 months ago by Kevin Blighe42k

Hi, I am using tophat+cufflinks(cuffquant+cuffdiff). I have the differentially expressed genes. I am lookin for the FPKM sd. Does any of cuffdiff output file contain this information?

ADD REPLYlink written 4 months ago by yff0

I'm with Kevin Blighe here. The cufflinks pipeline is no longer (and for a while now) a recommended approach for any DEG analysis. It has been proven to perform sub-optimal at best.

I'n not even sure if sd on FPKM is a valid thing. That would assume that there is a kind of 'mean/median' of FPKM which is biologically not making much sense.

ADD REPLYlink written 4 months ago by lieven.sterck4.8k
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