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SRA taxonomy analysis

Hi

I've downloaded the SRA metadata and taxonomy files from https://www.ncbi.nlm.nih.gov/sra/docs/sradownload/

I'm trying to query various SRA samples for this taxonomic analysis but can't find it in any of the tables/columns.

SRA taxonomy analysis

taxonomy sra
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written by Steve • Steve

2 answers

This data may only be available using BigQuery for SRA in cloud.

For more information on querying: https://www.ncbi.nlm.nih.gov/sra/docs/sra-cloud-based-taxonomy-analysis-table/

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written by GenoMax GenoMax

Thanks GenoMax I created an aws glue crawler to pull the data from s3://sra-pub-metadata-us-east-1/sra_tax_analysis_tool/

I wonder if it is an issue that the samples I'm interested in require dbGAP access. I do have dbGAP access to these particular samples but I wonder if they exclude all dbGAP samples those in the taxonomy table(s)?

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written by Steve • Steve

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