I have sequenced RNA from a bacterial culture grown under different conditions. The control sample was sequenced with IonTorrent, the other three other treatments were sequenced with Illumina HiSeq. Both samples were rRNA depleted before sequencing. I'd like to use TMM-normalized CPM to compare expression of different genes of interested due to not having replicates. Is that ok in principle or would there be a more suitable approach?
I noticed that many reads from IonTorrent data map to small RNA (5S, tRNA) which isn't the case for the Illumina data. As far as I understand, CPM normalizes by the total read count that mapped and would lead to a significant bias between IonTorrent and Illumina dat, correct? Any advice on how I could deal with this?