I am a newbie to RNAseq analysis. I am comparing (treatment vs control). Briefly, I mapped the RNA-seq reads to the reference genome using STAR and I used featureCounts to quantify the reads mapped to the reference genes and found the gene counts. Before I start the deferentially expression analysis, I would like to find the expressed genes. I use the command below and found 15463 genes, is it right to say, out of 24321 genes 15463 genes are expressed.
dds<-dds[rowSums(counts(dds)) > 0,]
dds<-dds[rowSums(counts(dds)) > 5]