I am doing some viral RNA-seq work and I got back bacterial rRNA contigs (e.coli and salmonella) when I used SPAdes. So how do I interpret this? I expected avian rRNA since it is the host but the bacterial ones are unexpected. Does this mean I have two different bacterial contaminates or does this mean I have two smaller contigs of avian rRNA that have a lot of similarity to these bacteria?
To do the target list I used the ncbi command line tools and requested just the top match back. So when I find these two sequences I blast'ed them individually thinking I would find it matching to a lot of different rRNAs but only e.coli and salmonella were returned.
Any advice would be appreciated.