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Hi! I have been using Kaiju for a while, and now I am interested in filtering fungal reads. For this, I used the Kaiju app in KBase and compared the results using two different databases: NCBI BLAST nr+euk (protein sequences from nr: Bacteria, Archaea, Viruses, Fungi, and microbial eukaryotes) and fungi (protein sequences from a representative set of fungal genomes). Based on the same samples, I would expect to have more fungal reads using the comprehensive database (nr since I thought RefSeq would be included in nr), but the fungal one results in way more hits. Please, what is the explanation for that?
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