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Old 10-02-2017, 06:51 AM   #1
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Location: Germany

Join Date: Oct 2017
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Default FPKM=0 resulted by Cuffdiff

Now, I am analyzing the RNA-seq data (20 samples).
I am using Tophat-Cufflinks line, and the calculation of FPKM has been successful.
Next, I tried to compare between 20 samples with Cuffmerge and Cuffdiff,
but I got the results which the FPKM value of all samples and genes are 0.

I could get the results seems correct, when I compared between only 2 samples, therefore, I guess that my command is correct.

Could you tell me some suggestions, if you have some ideas to solve this problem?

I am using Cufflinks ver2.1.1.
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