Tree of Life Profile Reads Submission

Prerequisites & Notes

Important

Note

  • Once reads have been submitted, they cannot be deleted.

  • Submit samples before uploading Reads manifests. See Samples submission for details.

  • Upload all required data files before submitting Reads manifests. See: Uploading Data Files.

Accessing the Reads Page

The Reads [3] page can be accessed via the Components button or via the components icon navigation pane when viewing another component’s page associated with a Tree of Life profile [1].

Using the Components Button

Click the reads-component-button component button in the Components column as shown below:

Reads profile component button

Reads component button (located under Tree of Life profiles)


Using the Components Icon Navigation Pane

The component icon navigation pane provides a quick access to other components associated with the same profile. It appears on the inner right pane of the screen when you are viewing a component’s page. The icons displayed in the navigation pane correspond to the components associated with the profile.

If you are unsure what each icon represents, you can perform any of the following:

  • Hover over the icon in the component icon navigation pane to see a tooltip with the component’s name

  • Refer to the component button image above

  • Refer to the What are profile components? FAQ

Note

  • The navigation pane will not display the icon associated with the page that is currently being viewed.

  • If a component has subcomponents, a dropdown menu is shown when at least two items are available. However, if you are viewing a subcomponent’s page and only one item remains, that item is displayed directly in the navigation pane.

Reads profile component icon

Navigation pane showing the Reads component icon

Upload Reads

  1. Click the dropdown menu to choose a checklist [4].

    Currently, only one option is available.

    Pointer to Reads checklist dropdown menu

    Pointer to dropdown menu for reads


    Hover over each option to view its description.


    Available reads checklist options within a Tree of Life profile

    Checklist options for read submissions


  2. Click the reads-blank-manifest-download-button-tol button to download a blank manifest [5].

    A manifest is a spreadsheet file used to record metadata for submission.

  3. Fill in the downloaded manifest then, click the add-reads-manifest-button-tol button to upload it from your local (computer) system.

    Warning

    If you are submitting a Reads manifest that includes the column, Sample, please ensure that the sample alias (i.e. sample name or accession number) is accurate. Once submitted, the value cannot be changed. Reads uploaded to COPO will also be sent to ENA.

    Note

    • The colour of the add-reads-manifest-button-tol button is based on the type of profile that you are making a submission to.

      See the Profile Types Legend section regarding the colour code for the various types of project profiles on COPO.

    • Please ensure that the manifest that you are uploading matches the checklist type selected in step 1. You will encounter errors if the uploaded manifest does not correspond with the selected dropdown menu checklist option.

    Tip

    For guidance on how to fill in the Reads manifest to submit paired reads, please see the Reads manifest for paired reads FAQ.

    Pointer to 'Add study from spreadsheet' button

    Click “Add study from spreadsheet” button to open an upload dialogue


  4. A dialogue is displayed. Click the reads-upload-button-tol button in the dialogue to choose the spreadsheet file from your local system.

    Upload Reads spreadsheet dialogue

    Click ‘Upload manifest’ button


  5. The uploaded data is shown in a preview before final submission. Click the finish-button button to finalise the upload.

    Dialogue with uploaded Reads data

    Reads upload preview


  6. The new reads data will be displayed on the Reads page after a successful validation.

    Reads data uploaded

    Reads page showing the uploaded data


Submit Reads

Note

  • Follow the steps in Upload Reads to upload data before proceeding with the submission.

  • The following repositories are supported for Reads submissions:

    • European Nucleotide Archive (ENA) via submit-record-button button

  1. After uploading data, select a row in the data table.

    Then, click the submit-record-button button to submit the selected record to European Nucleotide Archive (ENA).

    Note

    Please ensure that the selected record is under the desired checklist option. If not, choose another option from the dropdown menu, then select a row in the data table.

    Reads data uploaded

    Click Submit buton


  2. Wait for the submission process to be completed. The submitted record’s status and accessions can be viewed in the data table’s respective columns. See the sections below for details.

Make Data Public

  1. Submissions are private by default. You can make the data publicly accessible by referring to the steps in the Publishing Data at Profile Level section.

View Submission Status

Hint

The Data status & progress legend, located on the right side of the data table, shows the different stages of submission processing. Hover over the info-icon to see description for each status.

For more details, see the How can I check the status of my data submissions? FAQ section.

The submission will be scheduled for processing after the submit-record-button button is clicked. The row of the submitted record will be highlighted in green indicating that the submission has been successful.

If the submission was unsuccessful or has not been assigned any accessions, the table row will be highlighted in red. Its status is indicated in the following columns:

  • STATUS - Displays the European Nucleotide Archive (ENA) status assigned to the project

  • ENA FILE UPLOAD STATUS - Displays the ENA status assigned to the uploaded data files

  • ENA FILE PROCESSING STATUS - Displays the outcome after ENA has verified and validated the uploaded data files.

    Refer to the Checking ENA File Processing Status FAQ for more details

View Accessions

Accessions are unique identifiers assigned to submissions after they have been successfully submitted to public repositories.

The accession columns are:

  • STUDY ACCESSION - Displays the project accession assigned by European Nucleotide Archive (ENA)

  • RUN ACCESSION - Displays the accession assigned to the submitted reads by ENA

  • EXPERIMENT ACCESSION - Displays the experiment accession assigned to the project by ENA

Clicking any accession in the data table will open the corresponding record in the associated repository. You can also find the same record by searching for the accession directly in the repository.

Tip

Alternatively, click the accessions-component-icon icon located in the top-right corner of the data table to navigate to the Accessions page that displays accessions for all submissions.