Question: which file and column outputted from Cuffdiff corresponds to each sample FPKM standard deviation?
gravatar for yff
23 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 • 602 views
ADD COMMENTlink written 23 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 23 months ago by Kevin Blighe67k

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 23 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 23 months ago by lieven.sterck8.9k
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