Subtraction Updated September 1, 2020

Overview

Subtractions are whole genome references used for eliminating reads from the analysis that are likely to have originated from the host genome or non-pathogenic organisms associated with the host such as insects or fungi. A list of subtractions made can be found on the Subtraction Overview page. Subtraction Overview

Upload FASTA

Go to the Subtraction view via the main navigation bar. You should see the following:

“Main Subtraction View”

Click on the Files link in the left sidebar to go to the subtraction file manager.

“Subtraction File Manager

Upload the previously obtained FASTA file.

Create a Subtraction

Click on the Subtraction tab in the main navigation bar. New Subtraction

To create a new subtraction click the button next to the search bar. This will open up the subtraction creation dialog. Create Subtraction

Enter a unique name and an optional nickname, select the FASTA file, and click Start to start the job. Filled create subtraction dialog box

While the subtraction is being created it will have an Importing label. Importing

Wait for the job to complete before trying to use the new subtraction. You can view its progress by going to the Jobs view. Jobs View

The subtraction will have the Ready label when it is ready to use. Subtraction Ready

View a Subtraction

View detailed information about the subtraction by clicking on it. As you use the subtraction in samples, they will be added to the Linked Samples list. Subtraction Details

Edit a Subtraction

Click on Subtraction in the main navigation bar and click on the subtraction you would like to edit. Overview of Subtraction

Click on the icon on the subtraction details page to bring up the Edit Subtraction dialog box. Edit a Subtraction

Once a subtraction is made, the Unique Name and File cannot be changed. You are however, allowed to change the nickname of the subtraction. Nickname Added

The edits made on the subtraction will show up on the subtraction details page. Edits Shown on Subtractions Detail Page

Delete a Subtraction

Click on Subtraction in the main navigation bar and click on the subtraction that you wish to delete. Subtraction Overview

To delete the subtraction click on the icon on the subtraction details page. Delete Subtraction

A dialog box will then pop up to confirm the deletion; select Confirm. Confirm Deletion of Subtraction

After confirming the deletion of a subtraction, it will no longer be shown on the subtraction overview page. Post Deletion

Once you start using subtractions in samples and they become Linked Samples, you will not be able to delete the subtraction. Linked Samples