Im quite new to bioinformatics and linux in general. I have generated some RNAseq data using ONT minion 1d cDNA kit (PCS-109) to compare the transcriptome of cells expressing viral proteins which are stably transfected into the cells. As a control i just need to confirm the expression of these proteins within the cells and im not sure on the best method. I seen one way is to map to a human reference and then take the unmapped sequences and map them to the viral genome. But im not sure exactly how to do this and what alignment tools to use. Any help on this would be hugely appreciated!