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⇱ Command Line Tools for Genomic Data Science | Coursera

Command Line Tools for Genomic Data Science

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Command Line Tools for Genomic Data Science

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Gain insight into a topic and learn the fundamentals.
4.0

572 reviews

1 week to complete
at 10 hours a week
Flexible schedule
Learn at your own pace
87%
Most learners liked this course
Gain insight into a topic and learn the fundamentals.
4.0

572 reviews

1 week to complete
at 10 hours a week
Flexible schedule
Learn at your own pace
87%
Most learners liked this course

Build your subject-matter expertise

This course is part of the Genomic Data Science Specialization
When you enroll in this course, you'll also be enrolled in this Specialization.
  • Learn new concepts from industry experts
  • Gain a foundational understanding of a subject or tool
  • Develop job-relevant skills with hands-on projects
  • Earn a shareable career certificate

There are 4 modules in 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.

In this module, you will be introduced to Command Line Tools for Genomic Data Science

What's included

12 videos7 readings2 assignments

12 videos•Total 105 minutes
  • Basic Unix Commands 1: Content Representation•3 minutes
  • Basic Unix Commands 2: Files, Directories, Paths•7 minutes
  • Basic Unix Commands 3: File Naming•4 minutes
  • Basic Unix Commands 4: Content Creation•9 minutes
  • Basic Unix Commands 5: Accessing Content I•6 minutes
  • Basic Unix Commands 6: Accessing Content II•5 minutes
  • Basic Unix Commands 7: Redirecting Content•6 minutes
  • Basic Unix Commands 8: Querying Content•16 minutes
  • Basic Unix Commands 9: Comparing Content•11 minutes
  • Basic Unix Commands 10: Archiving Content•14 minutes
  • Basic Unix Commands 11: Practical Exercises I•13 minutes
  • Basic Unix Commands 12: Practical Exercises II•9 minutes
7 readings•Total 70 minutes
  • IMPORTANT: Setup the Virtual Machine for This Course•10 minutes
  • Welcome Message•10 minutes
  • Syllabus•10 minutes
  • VMBox (or Docker) Download and Instructions•10 minutes
  • Docker Image Download & Instructions•10 minutes
  • Pre-Course Survey•10 minutes
  • Module 1 Exam Instructions **IMPORTANT**•10 minutes
2 assignments•Total 60 minutes
  • Module 1 Quiz•30 minutes
  • Module 1 Exam•30 minutes

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

What's included

11 videos1 reading2 assignments

11 videos•Total 127 minutes
  • Sequences and Genomic Features 1: Molecular Bio Primer•6 minutes
  • Sequences and Genomic Features 2: Sequence Representation and Generation•11 minutes
  • Sequences and Genomic Features 3: Annotation•14 minutes
  • Sequences and Genomic Features 4.1: Alignment I•14 minutes
  • Sequences and Genomic Features 4.2: Alignment II•9 minutes
  • Sequences and Genomic Features 5: Recreating Sequences & Features•13 minutes
  • Sequences and Genomic Features 6: Genomic Feature Retrieval•6 minutes
  • Sequences and Genomic Features 7: SAMtools I•11 minutes
  • Sequences and Genomic Features 8: SAMtools II•10 minutes
  • Sequences and Genomic Features 9: BEDtools I•16 minutes
  • Sequences and Genomic Features 10: BEDtools II•16 minutes
1 reading•Total 10 minutes
  • Module 2 Exam Instructions **IMPORTANT**•10 minutes
2 assignments•Total 60 minutes
  • Module 2 Quiz•30 minutes
  • Module 2 Exam•30 minutes

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

What's included

8 videos1 reading2 assignments

8 videos•Total 55 minutes
  • Alignment & Sequence Variation 1: Overview•4 minutes
  • Alignment & Sequence Variation 2: Alignment & Variant Detection Tools•5 minutes
  • Alignment & Sequence Variation 3: VCF•12 minutes
  • Alignment & Sequence Variation 4: Bowtie•9 minutes
  • Alignment & Sequence Variation 5: BWA •5 minutes
  • Alignment & Sequence Variation 6: SAMtools (mpileup)•7 minutes
  • Alignment & Sequence Variation 7: BCFtools•8 minutes
  • Alignment & Sequence Variation 8: Variant Calling•5 minutes
1 reading•Total 10 minutes
  • Module 3 Exam Instructions **IMPORTANT**•10 minutes
2 assignments•Total 60 minutes
  • Module 3 Quiz•30 minutes
  • Module 3 Exam•30 minutes

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

What's included

8 videos2 readings2 assignments

8 videos•Total 75 minutes
  • Tools for Transcriptomics 1: Overview•6 minutes
  • Tools for Transcriptomics 2: RNA-seq•8 minutes
  • Tools for Transcriptomics 3.1: Tophat I•9 minutes
  • Tools for Transcriptomics 3.2: Tophat II •9 minutes
  • Tools for Transcriptomics 4: Cufflinks•10 minutes
  • Tools for Transcriptomics 5: Cuffdiff•17 minutes
  • Tools for Transcriptomics 6.1: Integrated Genomics Viewer I•8 minutes
  • Tools for Transcriptomics 6.2: Integrated Genomics Viewer II •7 minutes
2 readings•Total 20 minutes
  • Module 4 Exam Instructions **IMPORTANT**•10 minutes
  • Post-Course Survey•10 minutes
2 assignments•Total 60 minutes
  • Module 4 Quiz•30 minutes
  • Module 4 Exam•30 minutes

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Instructor

Instructor ratings
3.4 (59 ratings)
Johns Hopkins University
2 Courses•37,076 learners

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Showing 3 of 572

H
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Reviewed on Mar 30, 2021

Very engaging course indeed. However, assignments were much harder and needed time to solve.

LS
·

Reviewed on Apr 23, 2020

Some explanations are4 not completely clear. A good summary of what every tools does and of which rools should be used to tackle which situation would really beneficial

GV
·

Reviewed on Mar 13, 2016

Very informative course. Because I am new to this, it was at times confusing. But overall, great teaching and great experience. Thank you.

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