ABI OMICSS Guide 2021
  • Welcome
  • Week 1
    • Molecular Biology
      • Introduction to Biology
      • Macromolecules
      • DNA & RNA
      • Cell Division
    • Command-Line
      • Connecting to the Server
      • The Linux Command-Line For Beginners
      • The Bash Terminal
    • R Programming
      • Getting Started
      • The Basics
      • Data Types
    • Week 1 Exam
  • Week 2
    • Molecular Biology
      • DNA Proofreading And Repair
      • Telomeres and Telomerase
      • Genes
      • The One Gene, One Enzyme Hypothesis
      • Transcription
      • Translation
    • R Programming
      • Data Types (continuation)
      • Reading Data
      • Subsetting
      • Control Structures
      • Functions
      • Scoping Rules
    • Week 2 Exam
  • Week 3
    • Molecular Biology
      • tRNA and Ribosomes
      • Stages of Translation & Protein Targeting
      • Heredity
      • Probabilities In Genetics
    • R Programming
      • Loop Functions
      • Base Graphics
    • Statistics and R
      • The Basics
    • Week 3 Exam
  • Week 4
    • Molecular Biology
      • Interesting Cases of Genes
      • The Chromosomal Basis of Inheritance
      • Variation in Species
      • Phenotype plasticity
    • R Programming
      • Practice 2
      • Practice 3
    • Statistics and R
      • Random Variables and Probability Distributions
      • Central Limit Theorem
    • Week 4 Exam
  • Week 5
    • Statistics and R
      • Confidence Interval
      • Introduction to Inference
      • t-distribution and Comparing Means
      • Linear Models
    • Experimental Techniques
      • Polymerase Chain Reaction (PCR)
      • Gel Electrophoresis
      • Sanger Sequencing
      • NGS Sequencing
    • Week 5 Exam
  • Week 6
    • Statistics and R
      • Power
      • ANOVA
      • Covariance and Correlation
    • NGS
      • Basic Unix Commands
      • Sequences and Genomic Features
      • FastQC
      • Practice Exercises
    • Week 6 Exam
  • Week 7
    • Statistics and R
      • Monte Carlo Simulation
      • Exploratory Data Analysis
      • Linear Regression
    • NGS
      • BEDtools
      • Alignment and Sequence Variation
      • Integrated Genomics Viewer
    • Week 7 Exam
  • Week 8
    • NGS
      • Variant Calling With GATK
      • Practice 1
    • Week 8 Exam
  • Module Syllabi
  • Additional Resources
  • Conclusion
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  • Enroll in the Course
  • Configure VMBox
  • Install Exam Docs
  • Congratulations!

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  1. Week 1
  2. Command-Line

Connecting to the Server

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To start using the command-line, you first need to download and install VMBox, a virtual environment to host all our command-line activities. Follow the instructions below to complete this procedure.

Enroll in the Course

The installation instructions are found in the .

To get access to the instructions and the necessary files, you have to enroll in the course using the following instructions.

  1. Navigate to the course home page

  2. Click on the Enroll button

  3. If you plan to study data science beyond the scope of this guide, then feel free to proceed with the free trial initialization process and enter your financial credentials. If not, choose the "Audit course" option. Keep in mind, though, that we are going to refer to this course a lot later in the guide while exploring NGS.

Configure VMBox

Now, follow and complete the installation instructions for your machine. Return here once finished.

Install Exam Docs

In order to be able to complete the module exams and the other exercises in this guide, you need to have access to the exam files. You can find the files below. They work hand in hand with VMBox.

You do not need to install the files on your computer. The exams and other exercises provide all the links needed, however, it is a good idea to bookmark the page in your browser in case you need to look something up.

Congratulations!

If you made it here, then congratulations! You have successfully completed this section. Move to the next portion of the guide with the arrow buttons below.

Coursera course Command Line Tools for Genomic Data Science offered by Johns Hopkins University
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OMICSS 2021 Course FilesZenodo