Kraken2 and plusPFP (plant sample)

Question

[manekineko]

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?

[GenoMax]

I have RNA-seq from a plant species, I run a read classification with Kraken2

Why are you doing this? Are you looking to see what kind of "contamination" is present besides the plant you know/have?

[manekineko]

Yes, to see what viruses for example there is, but strange non of the plan reads are detected…..!?

[GenoMax]

Unless your plant is not similar to any of the genomes included in PlusPFP.

[manekineko]

Strange i know at least one genome is there in pluspfp from same plant devision…. But zero plant reads…