Taxonomic summary output

[cymon]

A question rather than an issue:

To what classification system does the "#OTU ID" values of column one of the *.merged_SSU.fasta.mseq.tsv taxonomic summaries of the MAPSeq output refer to? (They are not NCBI Taxid's, nor are they LTP/Silva IDs, and the MAPSeq documentation was no help...)

Thanks...

[Vkale1]

We use a reformatted version of the SILVA databases standardises to an 8 level taxonomy. The IDs can be found on our ftp e.g. http://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/silva_ssu-20200130.tar.gz .This folder has an otu file with the IDs. The information is the same as the file mentioned above: lineage and taxid.

[cymon]

Thanks Varsha, much appreciated. Cymon

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On Tue, 14 Mar 2023 at 17:27, Varsha Kale ***@***.***> wrote: We use a reformatted version of the SILVA databases standardises to an 8 level taxonomy. The IDs can be found on our ftp e.g. http://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/silva_ssu-20200130.tar.gz .This folder has an otu file with the IDs. The information is the same as the file mentioned above: lineage and taxid. — Reply to this email directly, view it on GitHub <#59 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAS6V4DKIANKQR2W4W4OWDW4CTBDANCNFSM6AAAAAAVZAG4RQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

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___________________________________________ Cymon J. Cox Senior Researcher Plant Systematics and Bioinformatics Digital Laboratory Centro de Ciencias do Mar (CCMAR) - CIMAR-Lab. Assoc. Mailing address: CCMAR - Centro de Ciencias do Mar, Universidade do Algarve Campus de Gambelas Edif. 7 8005-139 Faro Portugal Phone: +351 289800051 ext 7380 Fax: +351 289800051 Email: ***@***.*** Skype Name: cymon.cox (Location Faro, PT) @ccmar <https://ccmar.ualg.pt/users/cymon> | Google Scholar <https://scholar.google.co.uk/citations?user=f5M7DhkAAAAJ&hl=en&oi=ao> | Scopus <http://www.scopus.com/inward/authorDetails.url?authorID=7402112716&partnerID=MN8TOARS> | Orcid <http://orcid.org/0000-0002-4927-979X> | CienciaVitae <https://www.cienciavitae.pt/6B15-9771-1D04> GPG: Public key on keyserver.ubuntu.com

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