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Command Line Tools for Genomic Data Science

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Command Line Tools for Genomic Data Science

This course is part of Genomic Data Science Specialization

Instructor: Liliana Florea, PhD

32,912 already enrolled

Included with

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4 modules

Gain insight into a topic and learn the fundamentals.

571 reviews

1 week to complete

at 10 hours a week

Flexible schedule

Learn at your own pace

87%

Most learners liked this course

4 modules

Gain insight into a topic and learn the fundamentals.

571 reviews

1 week to complete

at 10 hours a week

Flexible schedule

Learn at your own pace

87%

Most learners liked this course

Skills you'll gain

Tools you'll learn

Details to know

Shareable certificate

Add to your LinkedIn profile

Assessments

8 assignments

Taught in English

91%

of learners achieved a positive career outcome

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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.

Module details

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

What's included

12 videos7 readings2 assignments

12 videosTotal 105 minutes

Basic Unix Commands 1: Content Representation3 minutes
Basic Unix Commands 2: Files, Directories, Paths7 minutes
Basic Unix Commands 3: File Naming4 minutes
Basic Unix Commands 4: Content Creation9 minutes
Basic Unix Commands 5: Accessing Content I6 minutes
Basic Unix Commands 6: Accessing Content II5 minutes
Basic Unix Commands 7: Redirecting Content6 minutes
Basic Unix Commands 8: Querying Content16 minutes
Basic Unix Commands 9: Comparing Content11 minutes
Basic Unix Commands 10: Archiving Content14 minutes
Basic Unix Commands 11: Practical Exercises I13 minutes
Basic Unix Commands 12: Practical Exercises II9 minutes

7 readingsTotal 70 minutes

IMPORTANT: Setup the Virtual Machine for This Course10 minutes
Welcome Message10 minutes
Syllabus10 minutes
VMBox (or Docker) Download and Instructions10 minutes
Docker Image Download & Instructions10 minutes
Pre-Course Survey10 minutes
Module 1 Exam Instructions **IMPORTANT**10 minutes

2 assignmentsTotal 60 minutes

Module 1 Quiz30 minutes
Module 1 Exam30 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 videosTotal 127 minutes

Sequences and Genomic Features 1: Molecular Bio Primer6 minutes
Sequences and Genomic Features 2: Sequence Representation and Generation11 minutes
Sequences and Genomic Features 3: Annotation14 minutes
Sequences and Genomic Features 4.1: Alignment I14 minutes
Sequences and Genomic Features 4.2: Alignment II9 minutes
Sequences and Genomic Features 5: Recreating Sequences & Features13 minutes
Sequences and Genomic Features 6: Genomic Feature Retrieval6 minutes
Sequences and Genomic Features 7: SAMtools I11 minutes
Sequences and Genomic Features 8: SAMtools II10 minutes
Sequences and Genomic Features 9: BEDtools I16 minutes
Sequences and Genomic Features 10: BEDtools II16 minutes

1 readingTotal 10 minutes

Module 2 Exam Instructions **IMPORTANT**10 minutes

2 assignmentsTotal 60 minutes

Module 2 Quiz30 minutes
Module 2 Exam30 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 videosTotal 55 minutes

Alignment & Sequence Variation 1: Overview4 minutes
Alignment & Sequence Variation 2: Alignment & Variant Detection Tools5 minutes
Alignment & Sequence Variation 3: VCF12 minutes
Alignment & Sequence Variation 4: Bowtie9 minutes
Alignment & Sequence Variation 5: BWA 5 minutes
Alignment & Sequence Variation 6: SAMtools (mpileup)7 minutes
Alignment & Sequence Variation 7: BCFtools8 minutes
Alignment & Sequence Variation 8: Variant Calling5 minutes

1 readingTotal 10 minutes

Module 3 Exam Instructions **IMPORTANT**10 minutes

2 assignmentsTotal 60 minutes

Module 3 Quiz30 minutes
Module 3 Exam30 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 videosTotal 75 minutes

Tools for Transcriptomics 1: Overview6 minutes
Tools for Transcriptomics 2: RNA-seq8 minutes
Tools for Transcriptomics 3.1: Tophat I9 minutes
Tools for Transcriptomics 3.2: Tophat II 9 minutes
Tools for Transcriptomics 4: Cufflinks10 minutes
Tools for Transcriptomics 5: Cuffdiff17 minutes
Tools for Transcriptomics 6.1: Integrated Genomics Viewer I8 minutes
Tools for Transcriptomics 6.2: Integrated Genomics Viewer II 7 minutes

2 readingsTotal 20 minutes

Module 4 Exam Instructions **IMPORTANT**10 minutes
Post-Course Survey10 minutes

2 assignmentsTotal 60 minutes

Module 4 Quiz30 minutes
Module 4 Exam30 minutes

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Instructor

Instructor ratings

(59 ratings)

Liliana Florea, PhD

Johns Hopkins University

2 Courses36,744 learners

Offered by

Johns Hopkins University

Learner reviews

5 stars
50.43%
4 stars
21.36%
3 stars
13.83%
2 stars
5.60%
1 star
8.75%

Showing 3 of 571

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

Reviewed on Jun 18, 2021

Leart a lot. Recommend all others this course. Lecturer also cool and explain every bit of course contents.

Reviewed on Jan 8, 2017

More in-depth explanation would be better. Reasonable projects, overall. Well structured.

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