Reads Submission

How to Submit Reads

Note

Once reads have been submitted, they cannot be deleted.
Files must be uploaded before a reads manifest can be submitted. See: How to Submit Files.

Accessing the Reads’ Web Page

The Reads’ [1] web page can be accessed from the Components button associated with a profile [2].

Use Components’ Button to Navigate to Reads’ Web Page

Click the button associated with a profile. Then, click the from the popup menu displayed as shown below:

Genomics Profile Components: Reads component button

Upload Reads

Hint

To download a blank Reads’ manifest template, click the button.
For guidance on how to fill in the Reads manifest to submit paired reads, please see the Reads manifest for paired reads FAQ.

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.

This is important because the Sample column serves as the key for each row in the Reads manifest. Each unique sample in the manifest corresponds to a different biosample.

Note

The colour of the add-reads-manifest-button button is based on the type of profile that you are submitting a Reads for. See the Profile Types Legend section regarding the colour code for the various types of project profiles on COPO.

On the Reads web page, click the checklist dropdown to view a list of available checklists that support Reads’ submission as shown below.

Please note that the checklist options may vary depending on the type of profile you are submitting reads for.

Reads’ web page: Checklist dropdown menu with checklist options displayed

An overview of each Reads checklist option is explained in the Reads’ checklist section.
Click button to add Reads’ from a spreadsheet for the chosen checklist as shown below:

Note

The colour of the button is based on the type of profile that you are submitting a Reads for. See the Profile Types Legend section regarding the colour code for the various types of project profiles on COPO.

Reads’ upload: Click ‘Add Reads’ from Spreadsheet’ button
An Upload Read Manifest dialog is displayed. Click the button to choose a file from your local system.

Reads’ upload: ‘Upload Read Manifest’ dialog
The uploaded manifest is shown in a table in the Upload Read Manifest dialog as shown below. Click the button to submit the reads manifest.

Reads’ upload: ‘Upload Read Manifest’ dialog with uploaded manifest
The new read(s) will be displayed on the Reads web page after a successful submission.

Hint

Reads records that are highlighted yellow indicate that the records are pending submission. The records will be highlighted green after a successful submission.

Reads’ upload: Reads’ web page displaying the uploaded read(s)

Submit Reads

Hint

The submitted read record will be highlighted green.

Click the desired reads records from the list of reads displayed on the Reads’ web page. Then, click the Submit button (located in the top-right corner of the table) as shown below:

Reads submitted successfully — **Reads submission: The Read has been submitted**

Hint

To view accessions associated with the submitted reads, click the Accessions button located in the top-right corner of the table.