how to map greengene ids to ncbi taxon ids ?

Question

[cvu]

Hi Biostars,

I am running QIIME for microbiome analysis from raw DNA sequencing data and I am getting greengenes ids in resulting biom table. now I want to map these greengene ids to ncbi_taxids.

Please help.

Thanks

Answer 1

[5heikki]

If it's gg_13_5 release, they provide a map to GenBank accessions on their site (gg_13_5_accessions.txt.gz). You can further map those to NCBI taxon IDs. Be aware that a large fraction of these get "bacteria: environmental sequences" etc. useless taxonomies. There are some maps on the NCBI ftp too, although I can't remember where exactly and what kind..

[cvu]

thanks for the reply hekiki.