Question: Searching RNA-seq reads against multiple organisms
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gravatar for gwilson9
3.8 years ago by
gwilson90
gwilson90 wrote:

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?

rna-seq • 828 views
ADD COMMENTlink written 3.8 years ago by gwilson90

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

ADD REPLYlink written 3.8 years ago by genomax76k
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