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DerrickWood / kraken2

The second version of the Kraken taxonomic sequence classification system
MIT License
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Kraken 2 use for metabolic pathways/genes of species in bulk RNA #446

Open ghs101 opened 3 years ago

ghs101 commented 3 years ago

Hi,

This is not an issue more a technical question. I know that kraken is able to find microbial species in bulk RNAseq. However, when I blast the reads of the found species they dont seem to be matching with the species sometimes and if they do its always the same gene for that specie. Is it possible to do pathway/gene analysis with kraken2 on bulk RNAsew data?

Thank you for the great work delivered with Kraken2!

xiaoyunguo commented 2 years ago

I have the same question of using Kraken2 with RNAseq data, I wonder if the data base should be built with RNA data instead, e.g. .rna.fna.gz instead of genomic.fna.gz in Refseq.