First of, I just want to say I've never used DESeq2 before and I'm new to R. I've a counts.htseq file I've created with none of the mentioned tools. I simply used bash to aggregate the gene counts of each of my samples in to one file, which i've called counts.htseq.
Now, i thought it would be a breeze to run deseq2, but the first thing i noticed before even running the first line of code, is that I need a sample information table or "coldata". The documentation does not explain what that means or how I can generate one applicable to my counts file.
So, what is this "coldata" object and what kind of sample information is it supposed to contain and how do I make it? The documentation assumes that this is clear, but its not.
My counts file has 118 samples and thousands of genes expression values (read counts). Please see image of counts.htseq2 below. I'd appreciate any help in this regard.