Searching RNA-seq reads against multiple organisms

Question

[gwilson9]

I'm searching RNA-seq data from a parasite that most certainly has host RNA contamination. If I am only interested in the parasite's alignment map do I only provide the genome index of that organism? Or would I make a concatenated genome index that I then filter for parasite reads?

[GenoMax]

If you have the host genome available then you could use a tool like BBSplit to bin your reads.