Searching RNA-seq reads against multiple organisms
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?
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gwilson9 •
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If you have the host genome available then you could use a tool like BBSplit to bin your reads.