Analysis of host-parasite mixed transcriptome
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9 months ago
Vitis ★ 2.4k

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?

RNA-Seq alignment • 243 views
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9 months ago
alex.zaccaron ▴ 200

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.

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Great! Thanks! If you put this in as an answer, I'll click "accept".

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9 months ago
GenoMax 99k

You should use bbsplit.sh from BBMap suite for this purpose. It will allow you to bin the reads to multiple genomes (and handle multi-mappers in intelligent ways). See this thread.

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