Question: NCBI Taxonomy IDs for Kraken-Silva Database
gravatar for josmos43
9 months ago by
josmos430 wrote:

I am trying to run Kraken2 on 16S data, using the Kraken2-Silva database (built with "kraken2-built --special silva). The taxonomic IDs listed in column 5 of the kraken report does not correspond to the NCBI Taxonomy. (I need the correct IDs to visualize the results with Krona)

I am trying to find a way to map the NCBI IDs to the SILVA IDs. I found some mappings on the Megan6 page but it does not resolve the taxonomic IDs for the lowest common ancestors (higher ranks).

I would appreciate any Ideas how to go about this issue. Ideally, I would like to replace the Taxonomic IDs in the Files the Kraken database is built with.

Maybe there is also a way to create the Krona-plot for Kraken-output without Tax-IDs (ktImportText instead of ktImportTaxonomy)?

rna-seq • 537 views
ADD COMMENTlink modified 5 months ago by lara.h.urban0 • written 9 months ago by josmos430

I solved the issue buy using "ktImportText" instead, creating the text file from the kraken report

ADD REPLYlink written 8 months ago by josmos430
gravatar for Asaf
9 months ago by
Asaf6.5k wrote:

You should have the NCBI taxonomy ID in the kraken2 database folder under the file . Can you post some examples for the output? I suspect you got taxonomy IDs but perhaps not in the desired level.

ADD COMMENTlink written 9 months ago by Asaf6.5k
gravatar for lara.h.urban
5 months ago by
lara.h.urban0 wrote:

The names.dmp file in the taxonomy folder of the kraken2 database folder contains the mapping of the SILVA IDs to the bacterial names; perhaps this helps?

ADD COMMENTlink written 5 months ago by lara.h.urban0
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