Metagenome assembled genomes (MAG) Analysis

Link to presentation

Once the MAGs are generated, here are some downstream analysis that you can perform

Step 1: Download the MAGs generated to laptop

• Goto - Click on this link to get MAGs
• Select “bin_20_seqs.fasta” and download

Step 2: Upload files to PATRIC

PATRIC is web service available for microbial genome annotations

Register

• First register for an account, if you dont already have one. Requires your name, and email. Should be quick

Setup workspace

• Once you have an account set up, login with your credentials
• Click on “Workspaces” on the top bar
• On the right corner of the window, there is a button to create a new workspace
• Type in “metagenomics-workshop 2022”, and save

Upload files

• This should open a new workspace, click on the link “Upload” on the top right corner of the workspace
• This will open a new pop up window, with the option “Select Files”. Click this option
• Navigate your laptop for the bin downloaded, and upload this file
• Change Upload Type on the pop up window from “Unspecified” to “Contigs”
• Then select “Start Upload”

Check the uploads

• Once all the files are uploaded, they will be listed in the workspace
  • Check the file sizes to confirm they were uploaded, shouldn’t be 0
  • Check the symbol next to the filetypes, it should look like two lines if not, then the filetype needs to be changed
    • To change filetype, click on file and click on “Edit type” to the right bar
    • Select contigs, and save
    • The symbol should be updated to the lines now

Annotating bins/MAGs

• In PATRIC, click on “Services” on the top bar, then “Annotation”
• This should opena new tab. Next to contigs, clik on the “folder icon”
• This will open a new pop up window that allows you to navigate through your worksapce
  • find the metagenomics-workshop 2022 folder
  • select “bin_20_seqs.fasta” and click on “OK”
• This will take you back to the Annotation window, fil the form with the below inforamtion
  • Domain: bacteria
  • Taxonomy ID 2
  • My label : Workshop bin20
  • Output folder: metagenomics-workshop 20022
  • Click on Annotate

Patience The command was submit to the cluster, waiting for the magic to happen

Downloading the protein sequences

• In the Annotation directory
• Click on “Bacteria workshop bin20.feature_protein.fasta”, and click on the option “Download” on the right bar

Next steps…

The next few steps are dependent on your research questions. So I will just demonostrate the some of the data PATRIC generates that could be useful

Here is a Youtube video recorded by Amber Skye on some downstream analysis that you can perform.