Closed cymon closed 1 year ago
Vkale1
commented
1 year ago 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
commented
1 year ago Thanks Varsha, much appreciated. Cymon
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.
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Cymon J. Cox
Senior Researcher Plant Systematics and Bioinformatics Digital Laboratory Centro de Ciencias do Mar (CCMAR) - CIMAR-Lab. Assoc.
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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...