2021-04-26-umich-rnaseqDemystified

Warming Up

In this module, we will:

• cover basic materials needed
• familiarize ourselves with remote computing
• prepare for later modules

Local vs remote exercise:

1. Become familiar with the different appearance of the local shell
2. Create local folder ~/workshop_rsd for results
3. Log in to the aws instance with ssh <username>@50.17.210.255
4. Become familiar with appearance of the remote shell

Click here for hints - Local vs remote exercise

1. Familiarize with local shell appearance

2. Create local folder for results

    mkdir ~/workshop_rsd
   

3. Log in to aws instance

    ssh <username>@50.17.210.255
   

4. Become familiar with the differences between local and remote shell

Click here for demonstration of local (git-bash on Windows) vs remote (AWS)

Orientation exercise

Note: We will provide additional time during this exercise to ensure that everyone is prepared to move forward.

Orientation exercise:

1. Log in (or confirm logged in) to aws instance
2. Ensure in home directory with cd
3. Use cp to copy the data from /rsd/data/ to your home directory
4. Use ls to view references
5. Use ls to view input fastq files
6. Use mkdir to create a folder for our analysis

Click here for solution

1. Ensure we're logged in to remote

    ssh <username>@50.17.210.255
   

2. Ensure we are in home directory

    cd
   

3. Copy data to our home directory

    cp -r /rsd/data/ ~/
   

4. View our references

    ls ~/data/refs
   

5. View our input fastq files

    ls ~/data/reads
   

6. Create a folder for our analysis

    mkdir ~/analysis
   

Bonus exercise:

1. Ensure we're on remote aws instance
2. run the command fortune | cowsay | lolcat

Optional and only for fun!

These programs are installed 'games' for entertainment purposes.

Details about `fortune | cowsay | lolcat`

fortune prints a random fortune

cowsay is a talking cow

lolcat is like cat but with a fun twist