4.0
stars
523 ratings

Liliana Florea, PhD

24,746 already enrolled

Offered By

Johns Hopkins University

About this Course

25,382 recent views

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.

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Shareable Certificate

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Approx. 12 hours to complete

English

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Skills you will gain

Bioinformatics
Samtools
Unix
Command-Line Interface

Flexible deadlines

Reset deadlines in accordance to your schedule.

Shareable Certificate

Earn a Certificate upon completion

100% online

Start instantly and learn at your own schedule.

Approx. 12 hours to complete

English

Could your company benefit from training employees on in-demand skills?

Try Coursera for Business

Instructor

Instructor rating

3.31/5 (50 Ratings)

Liliana Florea, PhD

Assistant Professor

McKusick-Nathans Institute of Genetic Medicine

24,746 Learners

1 Course

Offered by

Johns Hopkins University

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Syllabus - What you will learn from this course

Content Rating88%(2,211 ratings)

Week

Week 1

4 hours to complete

Basic Unix Commands

4 hours to complete

12 videos (Total 105 min), 5 readings, 2 quizzes

12 videos

Basic Unix Commands 1: Content Representation3m

Basic Unix Commands 2: Files, Directories, Paths7m

Basic Unix Commands 3: File Naming4m

Basic Unix Commands 4: Content Creation9m

Basic Unix Commands 5: Accessing Content I6m

Basic Unix Commands 6: Accessing Content II4m

Basic Unix Commands 7: Redirecting Content6m

Basic Unix Commands 8: Querying Content15m

Basic Unix Commands 9: Comparing Content11m

Basic Unix Commands 10: Archiving Content13m

Basic Unix Commands 11: Practical Exercises I13m

Basic Unix Commands 12: Practical Exercises II9m

5 readings

Welcome Message10m

Syllabus10m

VMBox Download & Instructions10m

Pre-Course Survey10m

Module 1 Exam Instructions **IMPORTANT**10m

2 practice exercises

Module 1 Quiz30m

Module 1 Exam30m

Week

Week 2

3 hours to complete

Week Two

3 hours to complete

11 videos (Total 127 min), 1 reading, 2 quizzes

11 videos

Sequences and Genomic Features 1: Molecular Bio Primer6m

Sequences and Genomic Features 2: Sequence Representation and Generation11m

Sequences and Genomic Features 3: Annotation14m

Sequences and Genomic Features 4.1: Alignment I13m

Sequences and Genomic Features 4.2: Alignment II9m

Sequences and Genomic Features 5: Recreating Sequences & Features12m

Sequences and Genomic Features 6: Genomic Feature Retrieval5m

Sequences and Genomic Features 7: SAMtools I11m

Sequences and Genomic Features 8: SAMtools II9m

Sequences and Genomic Features 9: BEDtools I15m

Sequences and Genomic Features 10: BEDtools II15m

1 reading

Module 2 Exam Instructions **IMPORTANT**10m

2 practice exercises

Module 2 Quiz30m

Module 2 Exam30m

Week

Week 3

2 hours to complete

Week Three

2 hours to complete

8 videos (Total 55 min), 1 reading, 2 quizzes

8 videos

Alignment & Sequence Variation 1: Overview4m

Alignment & Sequence Variation 2: Alignment & Variant Detection Tools5m

Alignment & Sequence Variation 3: VCF11m

Alignment & Sequence Variation 4: Bowtie9m

Alignment & Sequence Variation 5: BWA 4m

Alignment & Sequence Variation 6: SAMtools (mpileup)6m

Alignment & Sequence Variation 7: BCFtools8m

Alignment & Sequence Variation 8: Variant Calling5m

1 reading

Module 3 Exam Instructions **IMPORTANT**10m

2 practice exercises

Module 3 Quiz30m

Module 3 Exam30m

Week

Week 4

3 hours to complete

Week Four

3 hours to complete

8 videos (Total 75 min), 2 readings, 2 quizzes

8 videos

Tools for Transcriptomics 1: Overview6m

Tools for Transcriptomics 2: RNA-seq7m

Tools for Transcriptomics 3.1: Tophat I9m

Tools for Transcriptomics 3.2: Tophat II 8m

Tools for Transcriptomics 4: Cufflinks10m

Tools for Transcriptomics 5: Cuffdiff16m

Tools for Transcriptomics 6.1: Integrated Genomics Viewer I8m

Tools for Transcriptomics 6.2: Integrated Genomics Viewer II 6m

2 readings

Module 4 Exam Instructions **IMPORTANT**10m

Post-Course Survey10m

2 practice exercises

Module 4 Quiz30m

Module 4 Exam30m

Reviews

4.0

151 reviews

5 stars
51.24%
4 stars
21.79%
3 stars
13.76%
2 stars
4.97%
1 star
8.22%

TOP REVIEWS FROM COMMAND LINE TOOLS FOR GENOMIC DATA SCIENCE

by GVMar 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.

by ADAug 26, 2018

Very informative course. Only downside is that the example datasets/scripts are not provided (which I tend to find to be useful for learning informatics).

by WLJul 6, 2016

This is perhaps one of the most clearly taught courses I have had on Coursera. Thank you for putting in time to teach us!

by AMAug 21, 2019

Interesting course. I have used some of this tools for some time but I find their's still something new to learn

View all reviews

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What will I get if I subscribe to this Specialization?
When you enroll in the course, you get access to all of the courses in the Specialization, and you earn a certificate when you complete the work. Your electronic Certificate will be added to your Accomplishments page - from there, you can print your Certificate or add it to your LinkedIn profile. If you only want to read and view the course content, you can audit the course for free.
Is financial aid available?
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Command Line Tools for Genomic Data Science

About this Course

Skills you will gain