I am wondering what the best practices are analyzing host-parasite mixed transcriptomes. If I have mRNA-Seq data from infected host tissues that contain both host and parasite genomes, which would be the best way to tease them apart? Mapping to a combined reference (host + parasite), or mapping to the host genome first, collecting unmapped reads and mapping to parasite genome? What would be the implications of these options? When I get the real data, I could run tests with both approaches, but maybe someone already have some thoughts on this here?
In my case, I mapped the RNA-seq reads to both host and parasite genomes simultaneously, after concatenating their genomes. Then, I removed unmapped reads and reads with primary alignment to the host chromosomes (I was interested in the parasite). From my point of view, if you remove reads that map to the host genome without verifying if they map to the parasite genome, you could end up removing reads derived from parasite's genes that have highly conserved homologs in the host genome, even though such cases are rare.