Question: NCBI Taxonomy IDs for Kraken-Silva Database
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gravatar for josmos43
3 months ago by
josmos430
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 • 201 views
ADD COMMENTlink modified 3 months ago by Asaf5.6k • written 3 months ago by josmos430

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

ADD REPLYlink written 8 weeks ago by josmos430
0
gravatar for Asaf
3 months ago by
Asaf5.6k
Israel
Asaf5.6k wrote:

You should have the NCBI taxonomy ID in the kraken2 database folder under the file seqid2taxid.map . Can you post some examples for the output? I suspect you got taxonomy IDs but perhaps not in the desired level.

ADD COMMENTlink written 3 months ago by Asaf5.6k
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