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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.
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.