On 07/03/13 10:32, jjv5 wrote:
> Hello,
>
> I'd like to use the NCBI 16S set of sequences with Ray Meta to get a
> taxonomic profile (for comparing to another tool). It seems I should
> be able to do this easily enough based on the existing NCBI-Genomes
> scripts and files, but it the details escape me. The script
> generateTrees.sh demonstrates how to create fasta files name with a
> genbank accession, but how does one use these with the various
> taxonomy .tsv files generated under the NCBI-Genomes directory?
> Perhaps I am missing something obvious?
>
You can achieve this with these two options:
-search searchDirectory
Provides a directory containing fasta files to be searched in
the de Bruijn graph.
Biological abundances will be written to
RayOutput/BiologicalAbundances
See Documentation/BiologicalAbundances.txt
-with-taxonomy Genome-to-Taxon.tsv TreeOfLife-Edges.tsv Taxon-Names.tsv
Provides a taxonomy.
Computes and writes detailed taxonomic profiles.
See Documentation/Taxonomy.txt for details.
You need gi identifiers in your 16S fasta files to identify them, and the file
Genome-to-Taxon.tsv must contain relationships between gi identifiers and taxon
identifiers.
> Thanks,
> Jim
>
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Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
endpoint security space. For insight on selecting the right partner to
tackle endpoint security challenges, access the full report.
http://p.sf.net/sfu/symantec-dev2dev
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