4.0
stars
523 ratings

Liliana Florea, PhD

25,169 already enrolled

Offered By

Johns Hopkins University

About this Course

21,412 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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Earn a Certificate upon completion

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Coursera Labs

Includes hands on learning projects.

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Approx. 11 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.

Coursera Labs

Includes hands on learning projects.

Learn more about Coursera Labs

Approx. 11 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

25,169 Learners

1 Course

Offered by

Johns Hopkins University

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Syllabus - What you will learn from this course

Content Rating88%(2,222 ratings)

Week1

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 Representation3mBasic Unix Commands 2: Files, Directories, Paths7mBasic Unix Commands 3: File Naming4mBasic Unix Commands 4: Content Creation9mBasic Unix Commands 5: Accessing Content I6mBasic Unix Commands 6: Accessing Content II4mBasic Unix Commands 7: Redirecting Content6mBasic Unix Commands 8: Querying Content15mBasic Unix Commands 9: Comparing Content11mBasic Unix Commands 10: Archiving Content13mBasic Unix Commands 11: Practical Exercises I13mBasic Unix Commands 12: Practical Exercises II9m

5 readings

Welcome Message10mSyllabus10mVMBox Download & Instructions10mPre-Course Survey10mModule 1 Exam Instructions **IMPORTANT**10m

2 practice exercises

Module 1 Quiz30mModule 1 Exam30m

Week2

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 Primer6mSequences and Genomic Features 2: Sequence Representation and Generation11mSequences and Genomic Features 3: Annotation14mSequences and Genomic Features 4.1: Alignment I13mSequences and Genomic Features 4.2: Alignment II9mSequences and Genomic Features 5: Recreating Sequences & Features12mSequences and Genomic Features 6: Genomic Feature Retrieval5mSequences and Genomic Features 7: SAMtools I11mSequences and Genomic Features 8: SAMtools II9mSequences and Genomic Features 9: BEDtools I15mSequences and Genomic Features 10: BEDtools II15m

1 reading

Module 2 Exam Instructions **IMPORTANT**10m

2 practice exercises

Module 2 Quiz30mModule 2 Exam30m

Week3

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: Overview4mAlignment & Sequence Variation 2: Alignment & Variant Detection Tools5mAlignment & Sequence Variation 3: VCF11mAlignment & Sequence Variation 4: Bowtie9mAlignment & Sequence Variation 5: BWA 4mAlignment & Sequence Variation 6: SAMtools (mpileup)6mAlignment & Sequence Variation 7: BCFtools8mAlignment & Sequence Variation 8: Variant Calling5m

1 reading

Module 3 Exam Instructions **IMPORTANT**10m

2 practice exercises

Module 3 Quiz30mModule 3 Exam30m

Week4

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: Overview6mTools for Transcriptomics 2: RNA-seq7mTools for Transcriptomics 3.1: Tophat I9mTools for Transcriptomics 3.2: Tophat II 8mTools for Transcriptomics 4: Cufflinks10mTools for Transcriptomics 5: Cuffdiff16mTools for Transcriptomics 6.1: Integrated Genomics Viewer I8mTools for Transcriptomics 6.2: Integrated Genomics Viewer II 6m

2 readings

Module 4 Exam Instructions **IMPORTANT**10mPost-Course Survey10m

2 practice exercises

Module 4 Quiz30mModule 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 CWAug 5, 2020

There were some typos and confusion about the need not to follow the example code for Exam 4.

However, I thought that the course was good and useful overall.

Thank You!

by GNApr 8, 2018

A really hard introduction to bioinformatics pipelines, it was difficult but was stimulant!

by GYAug 28, 2017

Highly recommended.

I suggest you take it before "Genomic Data Science with Galaxy".

by LSApr 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

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