Submit the XML files to ENA

  1. Register for an ENA submission account if you do not already have one https://www.ebi.ac.uk/ena/submit/sra/#registration
  2. Upload your sequencing data to your account area
    • Follow one of the submission methods detailed on the following page http://ena-docs.readthedocs.io/en/latest/upload_01.html
      • The main options are to use the webin Java client, FTP transfer or the Aspera client. These will require you to have registered for an ENA submission account first.
      • Please read this page and make sure to use one of the supported file formats http://ena-docs.readthedocs.io/en/latest/format_01.html
    • Remember you will need to provide md5 checksum value for every file you upload to ensure the integrity of uploaded file, see http://ena-docs.readthedocs.io/en/latest/upload_01.html#file-md5-checksums
    • If you have a large number of files to upload, you may want to create a manifest file that can then be supplied to aspera (using '--file-list=/PATH/TO/FILELIST’) for example to list which files need to be uploaded. This can be created programatically in unix using a command similar to 'find /PATH/TO/BASESEQUENCINGDIRECTORY -name "*.fq" > asperafilelist.txt’.
  3. Verify XML validity using the ENA test service (https://www-test.ebi.ac.uk/ena/submit/drop-box/submit/). More detailed submission programatic instructions are here http://ena-docs.readthedocs.io/en/latest/prog_01.html#
    • Choose your experiment.xml, run.xml, study.xml and submission.xml files from the zip folder created by the conversion tool.
    • Input your username and password, username will be something like "Webin-45144".
    • Fix any errors that the test service reports, please contact faang-dcc@ebi.ac.uk if you have any issues that you cannot resolve.
    • Keep resubmitting until no more errors reported, should see /RECEIPT/@success="true".
  4. Once you have passed the test service continue to submission with ENA production service (https://www.ebi.ac.uk/ena/submit/drop-box/submit/)
    • Choose your experiment.xml, run.xml, study.xml and submission.xml files from the zip folder created by the conversion tool.
    • Input your username and password, username will be something like "Webin-45144".
    • Fix any errors that the test service reports, please contact faang-dcc@ebi.ac.uk if you have any issues that you cannot resolve.
    • Keep resubmitting until no more errors reported, should see /RECEIPT/@success="true".
  5. Receive and store XML receipt
  6. Check for validation fails post submission (files are not checked until after submission), so it may be some time before you are emailed regarding any errors or success.

Please contact FAANG DCC if you have any issues with any of the processes on this page.