ChickPea DEG Analysis

Question

[deepkumar1983]

Hi,

I have chickpea RNA-seq data of control vs treated without any replicate. I had used HTseqCount for count the gene and want to use edgeR for identifying DEG. My question is what should be the ideal value for dispersion parameter because it was mentioned in edgeR manual that for well-controlled experiments are 0.4 for human data, 0.1 for data on genetically identical model organisms or 0.01 for technical replicates. Any help will be appreciated.

Thanks

Dr. Deepak

[GouthamAtla]

Dispersion will be estimated from your data. You don't need to specify any value in edgeR. This gives an idea about the variation in your data across replicates.

[deepkumar1983]

Thanks for the reply. But I have no replicates.

[GouthamAtla]

You could use DESeq. It tries to estimate dispersion without replicates.