Strange question so a bit of background:
I have used a targeted RNAseq panel so it is essentially a huge PCR reaction with specific primers to around 600 genes. Which are subsequently subjected to next gene sequencing.
The output from the manufacturers website is essentially a table of gene identifiers (from refseq) with the number of counts associated to each gene.
So to normalise FPKM/RPKM is not valid as the fragments amplified with the specific primers do not relate to the size of the gene. I have therefor simply normalised by count per million (cpm) so am left with a list of 600 genes with the CPM from each sample.
My question is how to proceed from here using Galaxy to get differential expression analysis. I have 3 donors and 3 conditions. I would ideally like to get volcano plots with annotated genes. Perhaps the plots require a third party program which someone could suggest?