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2023-submit-data-to-ncbi's Introduction

Submit data to the public databases

  • Log into NCBI portal https://submit.ncbi.nlm.nih.gov/subs/sra/
  • Click ´New submission´
  • Ensure contact information is correct
  • Press continue
  • Fill in the page
    • Use an existing bioproject ID or create a new one
    • Did you already register the sample?
    • Select publication date
    • Press continue
  • If you did not already register a project
    • Provide Project title
    • Public description
    • Select relevance
    • Press continue
  • If you did not already register the samples
    • Select "Metagenome or environmental"
    • Press continue
    • Fill in the required fields: sample_name, organism, host, collection_date, geo_loc_name, lat_lon
    • Press continue
  • Download and fill out SRA metadata sheet
  • Upload sheet
  • Press continue
  • Select "FTP or Aspera Command Line file preload"
    • Get the aspera key onto your follder on the server
    • Edit the paths in the command example provided on the NCBI page
    • open a screen session on the server e.g. "screen -S NCBIupload"
    • Load the Aspera module on the server "module load Aspera-CLI"
    • Enter the upload command
    • Check that the upload starts as expected (We should have a bit less than 100 MB/s)
    • Detach from the screen session
    • Periodically check the upload progress
    • Select the data from the preload area
    • Press continue
  • Press finish

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