Downloading SRA/fastq files using NCBI variables
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9.1 years ago
moranr ▴ 290

Hi,

I have a big table for >100 genomes with species having the following info:

e.g.

#Organism/Name           TaxID     BioProject Accession     BioProject ID     Group     SubGroup     Size (Mb)     GC%     Assembly Accession     Chromosomes     Organelles     Plasmids     WGS       Scaffolds     Genes     Proteins     Release Date     Modify Date     Status       Center     BioSample Accession
Acanthisitta chloris     57068     PRJNA212877              212877            Animals   Birds        1035.88       41.6    GCA_000695815.1        -               -              -            JJRS01    53875         11365     9751         06/05/2014       05/09/2014      Scaffold     BGI        SAMN02318032

I would like to get an SRA file/ID so I can download the specific reads for the assembly that was used.

Is there a way of doing this using E-utils ?

Thanks

NCBI Data RNA-Seq Python • 2.4k views
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