Cuffdiff for DEGs

Question

[HaroonPakistan]

Hi, I am using cuffdiff for the Differential Gene Expression. Upon running the command, I see this problem. I have only three samples there is no replicate but my data is running accurately. I am confused, either it will cause a problem in the future or not?

Outputs:

No conditions are replicated, switching to 'blind' dispersion method
Inspecting maps and determining fragment length distributions.
Modeling fragment count overdispersion.

[Kevin Blighe]

Hi, you will not be able to publish this data, in my opinion. Having just 3 samples and no replicates is 'problematic'. Can you please show the commands that you are running? Thank you in advance, Muhammad

[HaroonPakistan]

Hi, I am sorry for the late reply. I understand my samples are not enough but this is what my professor said to do. I used this command.

cuffdiff -o diff_out -b genome.fa -p 20 --library-type fr-firststrand -L b73,f1,mo17 -u stringtie_merged.gtf b73.bam f1.bam mo17.bam 

[Kevin Blighe]

Great, and can you share some of the output? The message that you showed (above) seems to be a warning message, not an error.