Viewing Your Results

After you upload your files to our FTP server, we will process your files automatically.
  • Processing your files can take anywhere from a few hours to a few days (depending on the size of your submission).
  • You will receive a variety of emails while we're processing your files, and an "ERCC Final Processing" email will indicate that your processing is complete.
  • It is likely that your initial submission will fail for some reason (invalid metadata, some issue with your manifest file, etc.). This is totally normal!
    Read through our Troubleshooting guide if you receive a failure email.
  • You can then view your data results and metadata results.
    • Your data results will be located on the FTP server (and you will be able to access them through the Genboree Workbench).
    • Your metadata results will be located on the exRNA GenboreeKB.
    • Both data and metadata will also be available through the private, ERCC-only exRNA Atlas.

Locating Your Data Results on the Genboree Workbench

  • Log onto the Genboree Workbench using your Genboree user name and password.
  • Read the e-mail you received - it contains a handy ASCII graphic that will illustrate where to find your files.
  • Your results will be organized into individual folders (by sample).
  • You can find post-processing files generated by the exceRpt Post-Processing tool in the "postProcessedResults_v4.6.3" folder.
Important Notes:
  • You will not be able to access your original FTP submission (manifest / metadata archive / data archive) via the Genboree Workbench.
  • Anyone who wants access to the data results will need to be a member of the "exRNA Metadata Standards" Group on the Genboree Workbench.

Locating Your Data Results on the FTP Server

Preliminary Steps for New Users

  • In order to view your data results on the FTP server, you will need to send the exRNA Team an email requesting FTP access to the private Atlas Virtual FTP Area.
  • You should also include your Genboree username, as well as any other Genboree usernames that might need access to the files via FTP client.
    • If new users come along later and need access, that's OK - we can always add them later.
  • Once we have given you access to see the private Atlas Virtual FTP Area on your FTP client, you will be able to see all submissions to the Atlas.

Locating Your Result Files

  • After we have given you access to the private Atlas Virtual FTP Area, log into our FTP server at with your Genboree username and password.
  • When you log in, you should see a directory named Follow the path below to find your results:
    • /
  • Your results will be listed under the analysis name you gave in the manifest file (or with a generic, time-stamped name if you didn't give an analysis name).
  • If your samples fall under a different genome (mm10, for example), then the path above will have that genome instead of hg19.

Locating Your Original Submission

  • You will be able to find your original submission (manifest file / metadata archive / data archive) by going to your lab's shared directory (exrna-[pi ID]).
  • Then, navigate to the finished directory. Your files will be located in one of the subdirectories (specified in your ERCC Final Processing email).

Understanding Your Data Results

  • Regardless of whether you access your data results by Genboree Workbench or FTP client, there will be a number of folders located inside the folder with your Analysis name.
    • Each subfolder, except two, corresponds to a sample that you submitted for analysis.
    • One subfolder, named postProcessedResults_v4.6.3, contains post-processing results created by the exceRpt small RNA-seq Post-Processing tool.
      • This tool merges information from all of the different samples and creates useful visualizations (tables, plots).
      • To learn more about this tool, view the exceRpt Tutorial Page.
    • The other subfolder, named metadataFiles, contains copies of the metadata files submitted to the exRNA GenboreeKB for storage.
      • These files are not the same as the metadata documents you submitted, for the most part - they have been edited and added onto by the pipeline.
  • Within each sample's folder, there will be the results associated with that sample.
    • To learn more about how to interpret your results, view the exceRpt Data Analysis page.

Locating Your Metadata Results on the exRNA GenboreeKB

  • Click the Job document link given to you in your email. This document will contain all of the different document IDs associated with your job.
  • Click a given ID to be taken to that document. You can open the document in your current tab or in a new tab.
  • You can learn more about navigating the exRNA Genboree KB UI in GenboreeKB exRNA Metadata Tracking System - Navigating the Metadata UI.

Copying Your Submission to the Public Atlas

  • By default, your submission through the FTP Pipeline will be uploaded to the private, ERCC-only Atlas.
  • If you would like your submission to be available on the public Atlas (so that non-ERCC members can see it),
    please email Emily requesting that your submission be copied to the public Atlas.
  • Once the submission has been copied to the public Atlas, you will be able to find associated data and metadata files
    on the Genboree Workbench / FTP Server / GenboreeKB in the following locations:
    • Genboree Workbench: "Extracellular RNA Atlas" Group -> [Database listed in your manifest file] Database -> Files -> "exRNA-Atlas" -> exceRptPipeline_v4.3.3 -> [Analysis name]
    • FTP Server: / (please contact us if you don't have access)
    • GenboreeKB: "Extracellular RNA Atlas" project. More info can be found here: GenboreeKB exRNA Metadata Tracking System - Navigating the Metadata UI.

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