DEG (Differential expression gene) analysis

Question

[sooni]

Hello. I always thanks to your help.

My question may be a very basic question.

As far as I know, the DESeq2 package uses RNA sequencing data. I have data containing a list of genes (DNA) and counts of samples corresponding to each gene. The samples consisted of a control group and an experimental group. I would like to obtain data listing genes that are significantly different between control and experimental groups. I think I need to do DEG analysis, which package should I use? The package I am thinking about right now is edgeR. Is edgeR an appropriate package for DNA-level DEG?

Thank you for help!

Answer 1

[dsull]

What exactly is "DNA-level DEG"? That makes zero sense. DEG = Differential EXPRESSION of genes.

In any case, for RNA sequencing data, yes, edgeR and DESeq2 are both tools that were designed for DEG. You can use either of them for DEG as many of us here do.

[dsull]

Well, I guess expression could be measured from the DNA indirectly such as with RNA Pol II binding to DNA via ChIP-seq but then the OP should specify that.