Frequently Asked Questions
Hint
To view the entire answer to a question, collapse the answer by clicking the 
button below.
Assemblies
What are the types of files that are required for assembly submissions in COPO?
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See the European Nucleotide Archive’s (ENA’s) documentation for details about the types of files that can be submitted for assembly submissions.
How can I assign a locus tag to assemblies?
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Hint
Each profile in COPO is known as a study or project in ENA (after reads have been submitted).
Note
Reads submission must be done in order for a locus tag to be assigned to the project.
This is because a project submission is done to European Nucleotide Archive (ENA) once reads submission has been completed.
You can assign a custom locus tag when creating a profile in COPO. See the image below for guidance.
Profile form: Adding locus tag
If a locus tag is not assigned, ENA will automatically assign a locus tag to your assembly after it has been submitted in COPO and deposited to ENA.
See ENA’s documentation for more details. The documentation outlines rules that the locus tag prefix should conform to.
Dashboard
How can I view accessions after I have submitted samples, reads, or experiments in COPO?
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Hint
GenBank accession numbers follow the format
GCA_XXXXXXXXX. They are automatically assigned by ENA and can be viewed on the National Centre for Biotechnology Information (NCBI) website using the link:https://www.ncbi.nlm.nih.gov/datasets/genome/?bioproject=<project-id>where<project-id>is the project ID (also known as study ID or profile ID) associated with the profile used to submit the files in COPO.
Click the
button.The accessions dashboard will be displayed.
Alternatively, navigate to the Accessions dashboard.
Is there a way to analyse metadata submissions?
Yes, the following are ways to analyse metadata submissions:
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- Tree of Life dashboard
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Alternatively, click the
button.
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- Tree of Life inspection web page
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Alternatively, click the
button.
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- Tree of Life inspection by Genome Acquisition Lab web page
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Alternatively, click the
button.
Files
How do I know when data files that have been uploaded to COPO are public at European Nucleotide Archive (ENA)?
See Checking ENA File Processing Status section for more information.
Why can’t I upload more data files in COPO?
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If you cannot upload new files to COPO on the Files web page, it is likely that you have reached the maximum number of data files that can be uploaded.
Please delete some files to free up space for new files.
Other
When was the COPO project launched?
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In September 2014, the COPO project was launched under the Biotechnology and Biological Sciences Research Council (BBSRC) with the aim of improving open access to and management of data within plant research. It was known as Collaborative Open Plant Omics at that time and is based at the The Genome Analysis Centre (TGAC).
Now, the project is known as Collaborative OPen Omics. It is based at the Earlham Institute (EI) formerly known as TGAC.
2014 - 2022 |
2023 - PRESENT |
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See also
Download a seminar presentationwhich gives an overview of the evolution of the COPO project since its inception in 2014 to the present day
Who are the developers of the COPO project?
Click to view answer
Please see:
COPO Team section on the About web page of the COPO’s website for current software developers of the project
Former Team Members and Contributors section on the About web page of the COPO’s website for the previous developers and contributors of the project
Permits
Can I view or download permits that I have uploaded in COPO?
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Yes, permits can be retrieved and downloaded by selecting the desired sample record(s) on the Samples web page
Then, clicking the 
button on the web page.
Why am I unable to upload permit one after the other?
Click to view answer
Warning
If you have more than one permit file to upload, they must be uploaded at the same time i.e. after you have clicked the
button, navigate
to the directory where the permits are stored and CTRL + clickall of the permits so that all the permits are highlighted and uploaded at the same time.
All permit files have to be selected/opened from the directory and uploaded together not one after the other.
How can I resolve ‘Conflicting data…’ error when uploading permits in COPO after having uploaded a manifest?
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The error message Conflicting data is displayed when at least one of the following occurs:
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The permit filename provided in the manifest does not end with the extension
.pdfor.PDFResolution: Rename the name of the permit file so that it ends with the extension,
.pdfor.PDFthen, reupload the manifest -
In the uploaded manifest, different permit filenames are associated with the same SPECIMEN_ID
Resolution: Provide a unique permit filename for each SPECIMEN_ID or provide the same filename for permit files that are associated with the same SPECIMEN_ID in the manifest. Then, reupload the manifest.
Why do I encounter the error ‘No xx permit found for xx ‘SPECIMEN_ID’…Filename of permit must be named xx’ after having uploading the permit files?
Click to view answer
This error message occurs when at least one of the following occurs:
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The manifest uploaded requires multiple permit files but they were uploaded separately i.e. one after the other.
Resolution: Please refer to Why am I unable to upload permit one after the other? FAQ for more information.
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The permit filename uploaded from your local system actually ends with
.pdf.pdf(or.PDF.PDF) and not.pdf(or.PDF)Resolution: Ensure that the name of the permit file ends with the
.pdfor.PDFextension only.If you are using a Windows operating system (OS) to upload permits, Windows OS by default, hides file extensions which results in it not being visible to you.
If you would like to see the file extension, you can enable it by following these guidelines.
Reupload the manifest as well as the permit files after the resolutions have been made.
Profiles
How can I be added to a profile group?
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* Make a request to the :email:`COPO team
How can I create a profile on COPO?
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* Click the |add-profile-button| button then, fill in and save the form displayed. .. figure:: /assets/images/profile/profile_add_form.png :alt: Profile types dropdown menu :align: center :target: https://raw.githubusercontent.com/TGAC/COPO-documentation/main/assets/images/profile/profile_add_form.png :class: with-shadow with-border :width: 400px :height: 400px **Add Profile form: Choosing a Profile Type**
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View the following video to see how to create a profile.
How can I add a subproject to a profile on COPO?
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In the Add Profile form, choose the desired subproject(s) from the list of associated projects as shown below.
See the Secondary Projects section for information about the available subprojects.
Add Profile form: Selecting Associated Profile Type dropdown menu
How can I add a subproject or secondary project to a primary project in ENA/Biosamples?
Click to view answer
Contact the with the request providing the project accession of the child/subproject and the project accession of the parent/primary project.
How can I edit or delete a profile that I have created in COPO?
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Click the
icon that is associated with the desired profile.The option to edit or delete a profile record will be displayed once clicked.
The web page will refresh after the task has been completed successfully.
How many profiles can I have in COPO?
You can have as many profiles as needed to represent your research objects.
For instance, you can create a profile to represent work done as part of a grant, subproject within a project or a PhD project.
How can I view more profiles that I have created in COPO?
Scroll downwards on the web page.
More profiles that you have created will be loaded.
How can I view more information about a profile that I have created in COPO?
Click to view answer
Note
The
button will only be associated with a profile if the profile has at least one
of the following information.
Click the
button associated with the profile.-
After the button is clicked, a popup dialog will show at least one of the following information if it is available:
Release Status (if applicable)
Release Date (if applicable)
Associated Profile Type(s)
Sequencing Centre
Profile: View more information popup dialog
How can I navigate to the top of the web page after having loaded several work profiles?
Scroll upwards on the web page.
Alternatively, click the
button which automatically navigates
to the top of the web page.
How can I create components for a profile?
Click to view answer
Navigate to the work profile web page
Click the
buttonFill in then, save the form that is displayed
Click the
button associated with the profile record to view
the component of the action that was performed
How can I make profiles or projects public or visible in European Nucleotide Archive (ENA)?
Click to view answer
Hint
Profiles (in COPO) are referred to as projects or studies (in ENA).
See Releasing Profiles (Studies) section for more information.
How can I view released studies on European Nucleotide Archive (ENA)?
Click to view answer
Hint
Profiles (in COPO) are referred to as projects or studies (in ENA).
If you know the project accession and/or profile title, you can find the corresponding project on the Accessions dashboard. By clicking the hyperlink associated with the project accession, you will be navigated to the associated study record on ENA.
See also
Retrieving accessions section for more information.
What are the names of the sequencing centres whose samples are brokered through COPO?
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Currently, there are 20 sequencing centres whose samples are brokered through COPO.
Each COPO ERGA profile should be associated with a sequencing centre.
The following are the names of the sequencing centres:
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What happens when a profile is updated in COPO?
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When a profile is successfully updated in COPO, the changes made to the profile will be reflected in the research objects such as samples, reads, assemblies or files associated with the profile.
For example, if a profile is updated to include -
a new associated profile type, the new associated profile type will be displayed in the sample records associated with the profile.
a new ENA locus tag, the new ENA locus tag will be associate displayed in the reads, sequencing annotations and/ assembles associated with the profile.
Reads
How do I fill in the Reads manifest to submit paired reads?
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Ensure that the Reads manifest contains the following:
PAIRED as the value for the Library layout column
File names in the File name column separated by a comma
See below for a snapshot of a Reads manifest for paired reads:
Reads’ manifest for paired reads
What are the types of files that are required for read submissions in COPO?
Click to view answer
See the European Nucleotide Archive’s (ENA’s) documentation for details about the types of files that can be submitted for read submissions.
Samples
Why is the ‘Finish’ or ‘Confirm’ button not visible in the ‘Upload Spreadsheet’ dialog after the manifest is successfully uploaded and validated?
Click to view answer
This issue occurs because in the manifest uploaded, one or more of the permit required fields or columns is set
to Y. This means that permit files are required for the sample(s) within the manifest.
Resolution: Upload the permit files using the button first then,
The Finish button will be displayed in the Upload Spreadsheet dialog (once there are no errors) if uploading the manifest for the first time.
Alternatively, if the manifest is being updated, the Confirm button will be displayed in the Upload Spreadsheet dialog (once there are no errors).
How can I update values for samples that I have submitted in COPO?
Reupload the amended manifest.
Note
The manifest must be reuploaded in the same profile that the samples were submitted in.
If the manifest requires permits, the permits must also be reuploaded so that the samples’ updates can be processed.
The desired value(s) will be updated once the field value is not a compliance field [1].
See the Updating Samples section for information about which field values can be updated.
How to check the status of samples that have been accepted or rejected as a sample submitter?
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Option 1: The Status column in the samples data table will display the status of the sample record on the Samples web page.
Option 2: The Error column in the samples data table will display an error message if the sample record has been rejected or if there are any errors associated with the sample record.
Can I delete samples that have submitted?
Click to view answer
No, samples cannot be deleted after the manifest have been submitted.
Can I retrieve samples or the manifest that have been submitted?
Click to view answer
Yes, see the How to Download Submitted Sample Manifest section for more information.
How can I view images that have been uploaded?
How can I download permits that have been uploaded?
What are the formats that I can download samples in?
Click to view answer
The following are the formats that samples can be downloaded in:
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Microsoft Excel Spreadsheet format (
.xlsx)See the Downloading manifest in spreadsheet format section for more information.
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Comma-separated values (csv) format (
.csv)On the Samples web page, click the
button to download a manifest
in csv format.See How to access Samples web page section for guidance.
How can I submit virtual samples in COPO?
Click to view answer
Virtual samples are research objects that are submitted to COPO under a Genomics profile.
See the Submitting Virtual Samples section for more information.
Why do I get a ‘PROXY_TISSUE_VOUCHER_ID_FOR_BIOBANKING’ error when uploading or updating a manifest?
Click to view answer
If you encounter the error, The ID should be in the format of institute unique name:collection code:id or institute
unique name:id and separated by \"|\" and the ID should be registered already., when trying to upload or update
the field, PROXY_TISSUE_VOUCHER_ID_FOR_BIOBANKING, in a manifest, please ensure that the format of the ID is
institution_unique_name:collection_code:voucher_id institution_unique_name:voucher_Id.
Sample Managers
How can I be assigned as a sample manager?
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Make a request to the indicating the type of profile group that you would like to be assigned as a sample manager.
The permission will be granted after the request has been approved.
How can I know if I have been assigned as a sample manager?
Click to view answer
The
button will be displayed on the web page.The accept/reject samples web page will be displayed once the button is clicked.
Alternatively, if you can navigate to the Accept/Reject Samples’ web page with an Unauthorisation error web page being displayed then, you are a sample manager.
How can I search for a particular profile or sample on the Accept or reject web page?
Click to view answer
See Guidelines for Searching Profiles and Samples on the Accept or Reject Web Page section for guidelines on querying profiles and sample records on the Accept or Reject Samples web page.
How can I accept or reject samples that users have submitted?
Click to view answer
Note
See Accessing the Accept or Reject Samples web page section for guidelines on accessing the Accept or Reject Samples web page.
See Accepting or Rejecting Samples section for more information.
How can I download sample manifests that have been submitted by manifest providers or sample submitters?
Can I download permits that users have uploaded in COPO?
Click to view answer
Yes, on the Accept or Reject Samples web page, permits can be downloaded by selecting the desired sample record(s)
then, clicking the 
button on the web page.
See Downloading permits section for more information.
Can I view images that users have uploaded in COPO?
Click to view answer
Yes, on the Accept or Reject Samples web page, images can be viewed by selecting the desired sample record(s)
then, clicking the 
button on the web page.
See Viewing images section for more information.
If I belong to more than one sample manager manifest group, how can I view or accept samples that belong to them?
Click to view answer
Note
The manifest dropdown menu will only be displayed on the Accept or Reject samples web page if you as a sample manager, belongs to more than one sample manager manifest group.
If the dtol sample manager group dropdown menu option is selected, both Aquatic Symbiosis Genomics (ASG) profiles and Darwin Tree of Life (DToL) profiles will be displayed in the All profiles tab and/or Profiles for My Sequencing Centre the Accept or Reject samples web page will be displayed (if any exists).
Choose desired sample manager group from the manifest group dropdown menu.
-
Click the
button to accept or reject samples.
Accept or Reject samples: Email address prompt shown when a user logs into COPO for the first time
See Viewing images section for more information.
How do I know if sample records are awaiting another review by another sample manager?
Click to view answer
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If samples require more than one sample manager to accept or reject them, the samples will be displayed in the Pending Samples tab until all sample managers have accepted them. Once all sample managers have accepted the samples, the samples will be displayed in the Accepted Samples tab.
As shown in the image below, sample records that are awaiting another acceptance will be highlighted yellow and the date when the records have been accepted will be displayed in the Approval Date column in the samples data table.
Refer to the Associated TOL (Tree of life) Project column to view the associated project(s) that the sample record belongs to. See the image below for an illustration.
Sample record highlighted in yellow awaiting another acceptance
Approval date displayed in the ‘Approval Date’ column of the samples data table
In the example above, the sample record is associated with BGE
Hint
The Approval Date column displays the date when the sample record was accepted by the sample manager as well as the associated profile type that the sample manager belongs to.
The Associated TOL (Tree of life) Project column displays the associated project that the sample record belongs to.
After the sample record has been accepted by all sample managers, the sample record will be displayed in the Accepted Samples tab as shown in the image below.
Sample record after all sample managers have accepted it
Approval date updated in the ‘Approval Date’ column of the samples data table
In the example above, the sample record is associated with BGE and SANGER (associated) profile types. The sample managers assigned to both associated profile types have accepted the sample record and the approval date has been updated in the Approval Date column of the samples data table.
How to check the status of samples that have been accepted or rejected as a sample manager?
Click to view answer
Option 1: Accepted samples can be viewed in the Accepted Samples tab while rejected samples can be found in the Rejected Samples tab on the Accept or Reject Samples web page.
Option 2: The Status column in the samples data table will display the status of the sample record.
Option 3: The Error column in the samples data table will display an error message if the sample record has been rejected or if there are any errors associated with the sample record.
Option 4: The Status log will display a chronological list of the status of the sample record as shown in the images below. It is located on the right of the Accept or Reject Samples web page below the top navigation bar.
Sample record status log collapsed
Sample record status log expanded on hover
Hint
If you hover over the Status log, it will expand to display more information about the status of the sample record.
How can I get a better view of sample record information displayed on the Accept or Reject Samples web page?
Click to view answer
Click the 
button to toggle the profile panel visibility on the
Accept or Reject Samples web page to either hide the profile panel and view more sample records or show the
profile panel to view more profiles.