Kraken2 and plusPFP (plant sample)
I have RNA-seq from a plant species, I run a read classification with Kraken2 and PlusPFP DB which should include also plants, nevertheless i got only 30% classified reads and only to bacteria!? Am i choosing a wrong DB?
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manekineko •
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Why are you doing this? Are you looking to see what kind of "contamination" is present besides the plant you know/have?
Yes, to see what viruses for example there is, but strange non of the plan reads are detected…..!?
Unless your plant is not similar to any of the genomes included in PlusPFP.
Strange i know at least one genome is there in pluspfp from same plant devision…. But zero plant reads…