which file and column outputted from Cuffdiff corresponds to each sample FPKM standard deviation?

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5.3 years ago

yff • 0

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?

Thanks

RNA-Seq cuffdiff cufflinks sd FPKM • 1.2k views

ADD COMMENT • link 5.3 years ago by yff • 0

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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 REPLY • link 5.3 years ago by Kevin Blighe 87k

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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 REPLY • link 5.3 years ago by yff • 0

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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 REPLY • link 5.3 years ago by lieven.sterck 15k

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