Create a Subtraction Updated September 1, 2020

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.

    “Download Arabidopsis 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.

    Empty subtraction list

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

    “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.

    Empty subtraction list

  2. Click the button

    This will open the subtraction creation dialog.

    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.

    Filled Creation Dialog

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

    Subtraction Importing

  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.

    Subtraction Job in Progress

    The job will look like this when it is complete:

    Subtraction Job Complete

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

    Subtraction Ready

  5. Click on the subtraction to view its details

    Subtraction Detail