Error while running the transcript count file obtained using StringTie on DeSeq

I obtained the transcript count file using StringTie and now I am trying to run the count file on DeSeq2 using galaxy server. I am getting the following error.

The design matrix has the same number of samples and coefficients to fit, so estimation of dispersion is not possible. Treating samples
as replicates was deprecated in v1.20 and no longer supported since v1.22.

I don’t know how to fix this error, please help!

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Hi @vedantbharti,
how many replicates do you have for each condition? it indicates that it is not possible to perform any statistical analysis.

I have 1 transcript count file for each factor level. I have 2 factor levels. One wild type and another with one particular gene knocked out. Please help!

HI @vedantbharti,
you need to provide more than one replicate, otherwise the statistical analysis is not possible.


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