Best R program to use for RNA seq analysis

Question

We have an RNA seq taken from a the same tissue in two different developmental stages. We have one gene, with the number of reads from stage A and stage B, and we want to see which genes are differentially expressed.

After performing RNA-seq, I am left with a CSV file containing a list of genes and the amount of reads in two different cell types. We have one list of genes, with the number of reads in Stage A in one column and the number of reads in Stage B in another column. We are looking to see what types of genes are differentially expressed in the two stages.

I have used DESeq2, but I'm not sure if this is the best/correct to analyze what I am looking for.

What is the best package to analyze the data for significant differential gene expression?

Thanks

Answer 1

DESeq2 works for that. Unless you literally have only two samples.

There is no statistically sound way of analyzing DE genes with literally only two samples. This is a bad experimental design, suitable for only the roughest of exploratory purposes. Only the most obvious differences (that you probably knew already) are likely to be borne out in a legitimate experiment.