What is the best way to make mapping of RNA virus from transcriptomic data?

Question

[Lissa Cruz Saavedra]

I am mapping an RNA virus using transcriptomic data. However, when I mapped the reads with BWA I got some reads in the final bam output, otherwise, when I mapped employing TopHat the bam output was empty. I would like to know, what is the best way to map RNA virus?

Thanks in advance for the answer.