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.

Find source FASTA

We will use the Arabidopsis thaliana genome as a subtraction in this tutorial.

1. Go to the Ensembl Genomes FTP site for Arabidopsis

   Download the unmasked version of the genome.

   

Upload FASTA

1. Go to the Subtraction view via the main navigation bar

   There will be a warning indicating that no subtraction has been created.

   

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

   

3. Upload the previously obtained FASTA file.

Create Subtraction

1. Go to the Subtraction view via the main navigation bar

   There will be a warning indicating that no subtraction has been created.

   

2. Click the button

   This will open the subtraction creation dialog.

   

3. Enter information for the new subtraction

   Give it a unique name and an optional nickname and select the uploaded FASTA file. Click the Start button to start the job.

   

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

   

4. Wait for the job to complete before trying to use the new subtraction

   You can view the creation progress by going to the Jobs view.

   

   The job will look like this when it is complete:

   

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

   

5. Click on the subtraction to view its details