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NGS for natural scientist
  • 1. Preface
    • How to use this book
    • Motivation
    • Genomic data science as a tool to biologist
    • Next Generation Science (also NGS)
  • 2. Getting started
    • A step by step pipeline tutorial
    • Sequencing chemistry explained by Illumina
    • Joining a course
    • RNA quality and Library prep
    • (optional) My click moment about "Why Linux"
  • 3. Good-to-know beforehand
    • Experiment design
    • Single-end and Paired-end
    • Read per sample and data size
    • Normalization - RPKM/FPKM/TPM
    • Gene annotation
  • 4. Setting up terminal
    • My Linux terminal
    • Linux environment
    • R and RStudio
    • PATH
  • 5. FASTQ and quality control
    • Getting FASTQ files from online database
    • FASTQ quality assessment
  • 6. Mapping/alignment and quantification
    • Salmon
    • DESeq2
  • 7. Visualization
  • 8. Single cell RNA-Seq
  • 9. AWS cloud and Machine Learning
    • Machine Learning in a nutshell
    • R vs Python
    • Setting up ML terminal
    • Data exploration
  • (pending material)
    • graphPad
    • readings for ML
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  • Setting up Ubuntu
  • Using Windows and Linux at the same time
  1. 4. Setting up terminal

Linux environment

I fell in love with Linux only when I reach my mid-30s. Love at the first sight does not apply in this situation.

PreviousMy Linux terminalNextR and RStudio

Last updated 2 years ago

Setting up Ubuntu

There are many Linux distributions and the exact reason for preferring Ubuntu is, none. I started Liunx-ing roughly 20 years ago and I was introduced to Redhat at the time. Then the next thing I remember is somewhere around 4, 5 years ago I was doing some and I would like to try my hand so I set up a dual boot Ubuntu at home. Of course there is something called by now but cheminformatics is still fascinating and super relevant especially if you work at molecular scale.

Essentially, you can make a bootable USB/DVD from the above site and plug and play Ubuntu. You can also try it right out using the media without installation.

Using Windows and Linux at the same time

Like I said I have 2 computers at home, one is Windows one is Ubuntu. It is very obvious that I am making the Ubuntu set up as my exclusive terminal that while I surf the web and youtube-ing on Windows, the Linux guy is calculating my sequencing data for me. That formulates to

  1. Remote access

  2. File transfer over LAN

1. Remote access

Remote accessing a desktop is something quite antique and you can easily Google hundreds if not thousands of webpage which talks about it. But with the technology advancement it has became easier than ever to remoting for my purpose. My aim is to

PC -> Linux

The setup is easy if you are using Windows 10, and the user experience is AWESOME.

You can stop by for better reference. I mean I think I can trust the official Ubuntu site for something involve network security. Anyway I logged in what I actually have done. I intend to avoid outdated information so what I did was

[Linux Terminal] 1. sudo apt install ufw (This is to install the uncomplicated firewall, which is not a lie to me)

[Linux Terminal] 2. sudo ufw allow from 192.168.1.1 to any port 3389 (replace 192.168.1.1 with the PC ip or you can do any to any port 3389)

[Linux Terminal] 3. sudo service ufw status to check if the ufw is running. sudo systemctl start ufw to fire it up and sudo systemctl stop ufw to kill it.

[Linux Terminal] 4. sudo ufw status numbered to check which port has been activated. sudo ufw delete 1 to delete the rule number 1, for example.

[Windows 10] 5. Fire up the Remote Desktop Connection application and connect to Linux using corresponding ip address. Login is the same to the user that you set in Linux.

2. File transfer via LAN

Assuming that you have installed ufw and you know how to operate it.

And I can now run packages on one system and work on entire different task on another. Busy man.

My set up is done via my router so they both are in the same LAN. And you know what, the text that I copied from Windows 10 can be pasted in Liunx during remoting. A-W-E-S-O-M-E (Carol/Cheryl from , awesome shows by the way)

[Linux Terminal] 1. sudo ufw allow ssh (This is to allow ssh and transfer data using sFTP) [Linux Terminal] 2. sudo service ssh status to check if the ssh is running. sudo systemctl start ssh to fire it up and sudo systemctl stop ssh to kill it. [Windows 10] 3. Install and FileZilla. Do not need to follow it to the letter because this site is dedicated to their own FTPs. [Windows 10] 4. Connect to the Linux system using Site Manager and transfer files by drag and drop.

https://ubuntu.com/download/desktop
protein folding prediction
Alphafold
here
ARCHER
setup