Command Line Tools for Genomic Data Science

About this course: Introduces to the commands that you need to manage and analyze directories, files, and large sets of genomic data. This is the fourth course in the Genomic Big Data Science Specialization from Johns Hopkins University.

Created by:  Johns Hopkins University

  • Liliana Florea, PhD
    Taught by:  Liliana Florea, PhD, Assistant Professor
    McKusick-Nathans Institute of Genetic Medicine
Basic Info
Course 5 of 8 in the Genomic Data Science Specialization.
How To PassPass all graded assignments to complete the course.
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Basic Unix Commands
In this module, you will be introduced to command Line Tools for Genomic Data Science 
12 videos5 readings
  1. Reading: Welcome Message
  2. Reading: Syllabus
  3. Reading: VMBox Download & Instructions
  4. Reading: Pre-Course Survey
  5. Video: Basic Unix Commands 1: Content Representation
  6. Video: Basic Unix Commands 2: Files, Directories, Paths
  7. Video: Basic Unix Commands 3: File Naming
  8. Video: Basic Unix Commands 4: Content Creation
  9. Video: Basic Unix Commands 5: Accessing Content I
  10. Video: Basic Unix Commands 6: Accessing Content II
  11. Video: Basic Unix Commands 7: Redirecting Content
  12. Video: Basic Unix Commands 8: Querying Content
  13. Video: Basic Unix Commands 9: Comparing Content
  14. Video: Basic Unix Commands 10: Archiving Content
  15. Video: Basic Unix Commands 11: Practical Exercises I
  16. Video: Basic Unix Commands 12: Practical Exercises II
  17. Reading: Module 1 Exam Instructions **IMPORTANT**
Graded: Module 1 Quiz
Graded: Module 1 Exam
Week Two
In this module, we'll be taking a look at Sequences and Genomic Features in a sequence of 10 presentations.  
11 videos1 reading
  1. Video: Sequences and Genomic Features 1: Molecular Bio Primer
  2. Video: Sequences and Genomic Features 2: Sequence Representation and Generation
  3. Video: Sequences and Genomic Features 3: Annotation
  4. Video: Sequences and Genomic Features 4.1: Alignment I
  5. Video: Sequences and Genomic Features 4.2: Alignment II
  6. Video: Sequences and Genomic Features 5: Recreating Sequences & Features
  7. Video: Sequences and Genomic Features 6: Genomic Feature Retrieval
  8. Video: Sequences and Genomic Features 7: SAMtools I
  9. Video: Sequences and Genomic Features 8: SAMtools II
  10. Video: Sequences and Genomic Features 9: BEDtools I
  11. Video: Sequences and Genomic Features 10: BEDtools II
  12. Reading: Module 2 Exam Instructions **IMPORTANT**
Graded: Module 2 Quiz
Graded: Module 2 Exam
Week Three
In this module, we'll be going over Alignment and Sequence Variation in another sequence of 8 presentations. 
8 videos1 reading
  1. Video: Alignment & Sequence Variation 1: Overview
  2. Video: Alignment & Sequence Variation 2: Alignment & Variant Detection Tools
  3. Video: Alignment & Sequence Variation 3: VCF
  4. Video: Alignment & Sequence Variation 4: Bowtie
  5. Video: Alignment & Sequence Variation 5: BWA
  6. Video: Alignment & Sequence Variation 6: SAMtools (mpileup)
  7. Video: Alignment & Sequence Variation 7: BCFtools
  8. Video: Alignment & Sequence Variation 8: Variant Calling
  9. Reading: Module 3 Exam Instructions **IMPORTANT**
Graded: Module 3 Quiz
Graded: Module 3 Exam
Week Four
In this module, we'll be going over Tools for Transcriptomics in a sequence of 6 presentations. 
8 videos2 readings
  1. Video: Tools for Transcriptomics 1: Overview
  2. Video: Tools for Transcriptomics 2: RNA-seq
  3. Video: Tools for Transcriptomics 3.1: Tophat I
  4. Video: Tools for Transcriptomics 3.2: Tophat II
  5. Video: Tools for Transcriptomics 4: Cufflinks
  6. Video: Tools for Transcriptomics 5: Cuffdiff
  7. Video: Tools for Transcriptomics 6.1: Integrated Genomics Viewer I
  8. Video: Tools for Transcriptomics 6.2: Integrated Genomics Viewer II
  9. Reading: Module 4 Exam Instructions **IMPORTANT**
  10. Reading: Post-Course Survey
Graded: Module 4 Quiz
Graded: Module 4 Exam
How It Works
Each course is like an interactive textbook, featuring pre-recorded videos, quizzes and projects.
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Johns Hopkins University
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