Question: how to map greengene ids to ncbi taxon ids ?
0
gravatar for cvu
3.2 years ago by
cvu130
India
cvu130 wrote:

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

ADD COMMENTlink modified 3.2 years ago by 5heikki8.4k • written 3.2 years ago by cvu130
1
gravatar for 5heikki
3.2 years ago by
5heikki8.4k
Finland
5heikki8.4k wrote:

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..

ADD COMMENTlink modified 7 months ago by RamRS21k • written 3.2 years ago by 5heikki8.4k

thanks for the reply hekiki.

ADD REPLYlink written 3.2 years ago by cvu130
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