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

• 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 Language English How To Pass Pass all graded assignments to complete the course. User Ratings 4.1 stars Average User Rating 4.1See what learners said Coursework

Each course is like an interactive textbook, featuring pre-recorded videos, quizzes and projects.

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Syllabus


WEEK 1


Basic Unix Commands
In this module, you will be introduced to command Line Tools for Genomic Data Science


12 videos, 5 readings expand

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 2


Week Two
In this module, we'll be taking a look at Sequences and Genomic Features in a sequence of 10 presentations.


11 videos, 1 reading expand

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 3


Week Three
In this module, we'll be going over Alignment and Sequence Variation in another sequence of 8 presentations.


8 videos, 1 reading expand

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 4


Week Four
In this module, we'll be going over Tools for Transcriptomics in a sequence of 6 presentations.


8 videos, 2 readings expand

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