Bioinformatics assignment

Basic processing of NGS genomic data

The purpose of this exercise is to learn how to apply the steps we taught you about in the tutorials. At first the assignment might seem a little overwhelming/unfamiliar. Don’t worry! This is why we have made a working example to accompany the project. I will go through the steps that you have to go through in the worked example below (updates will be applied before you have to start each step).

Why have I been dropped in at the deep end?/I haven’t done some of this stuff before!

If you speak to just about any bioinformatician they will tell you that the best way to learn bioinformatics is through trial and error. There is a worked example here, so you shouldn’t go too far off piste. Also, you have your own VM and lots of space, you can’t really go wrong!

1) Find a suitable microbial genomic data set on which you wish to work: The data set should not be too ambitious in size and can be an outbreak data set or a data set from some evolutionary analyses

You can see my e-lab book here (remember that my IP address and folder names will be different):

I chose this paper for my data:

My basis is that;

  • The reads are available in the ENA
  • There is a well characterised, publically available, reference genome referred to in the paper
  • There is a phylogenetic tree in the paper that I can use for comparisons later

At this point I also logged into my VM to check that I can access it and that the extra storage has been allocated to me.

ssh ubuntu@

I started a screen session to ensure that I can shut my terminal without killing my jobs (remember you only need to do this once).

screen -S assignment

When you secure shell (ssh) into your terminal another time you can check what screens you have by typing

screen -ls

To check whether you are in a screen session try this:

echo $STY

I can see that I am in a screen session called 25794.assignment

If I wasn’t in that screen session but I wanted to attach it I would use this command:

screen -dr assignment

I now want to check that my VM is mounted to the extra storage and that I can access it

ls /coursework

I am going to work from my folder

cd /coursework/tutor

I need to make a new directory for this assignment

mkdir assignment
cd assignment

####Whoop! that completes part one!