4.0
stars
506 ratings

Liliana Florea, PhD

23,700 already enrolled

Offered By

Johns Hopkins University

About this Course

22,671 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.

Flexible deadlines

Reset deadlines in accordance to your schedule.

Shareable Certificate

Earn a Certificate upon completion

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Approx. 12 hours to complete

English

Subtitles: Arabic, French, Portuguese (European), Italian, Vietnamese, German, Russian, English, Spanish

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

Subtitles: Arabic, French, Portuguese (European), Italian, Vietnamese, German, Russian, English, Spanish

Instructor

Instructor rating

3.34/5 (48 Ratings)

Liliana Florea, PhD

Assistant Professor

McKusick-Nathans Institute of Genetic Medicine

23,700 Learners

1 Course

Offered by

Johns Hopkins University

The mission of The Johns Hopkins University is to educate its students and cultivate their capacity for life-long learning, to foster independent and original research, and to bring the benefits of discovery to the world.

Syllabus - What you will learn from this course

Content Rating87%(2,139 ratings)

Week

Week 1

4 hours to complete

Basic Unix Commands

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

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

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

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

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

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

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

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

146 reviews

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2 stars
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1 star
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TOP REVIEWS FROM COMMAND LINE TOOLS FOR GENOMIC DATA SCIENCE

by EKMar 3, 2019

Excellent Introduction to Command Line Tools used in High Throughput Sequencing Analysis.

by HPMar 10, 2022

Course explanation is good but some topics are not updated like mplieup is now not included in samtools and they didnot update information. Instructor taught lectures very well.

by SAJul 13, 2018

Great resource to learn unix codes and prepare your self for analysing genomic data

by NMJun 18, 2021

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

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?
Yes. In select learning programs, you can apply for financial aid or a scholarship if you can’t afford the enrollment fee. If fin aid or scholarship is available for your learning program selection, you’ll find a link to apply on the description page.

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Command Line Tools for Genomic Data Science

About this Course

Skills you will gain