About this Course
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Approx. 26 hours to complete


Subtitles: English

Skills you will gain

BioinformaticsSamtoolsUnixCommand-Line Interface

100% online

Start instantly and learn at your own schedule.

Flexible deadlines

Reset deadlines in accordance to your schedule.

Approx. 26 hours to complete


Subtitles: English

Syllabus - What you will learn from this course

3 hours to complete

Basic Unix Commands

12 videos (Total 105 min), 5 readings, 2 quizzes
12 videos
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
VMBox Download & Instructions10m
Pre-Course Survey10m
Module 1 Exam Instructions **IMPORTANT**10m
2 practice exercises
Module 1 Quiz20m
Module 1 Exam34m
3 hours to complete

Week Two

11 videos (Total 127 min), 1 reading, 2 quizzes
11 videos
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 Quiz20m
Module 2 Exam40m
2 hours to complete

Week Three

8 videos (Total 55 min), 1 reading, 2 quizzes
8 videos
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 Quiz20m
Module 3 Exam48m
3 hours to complete

Week Four

8 videos (Total 75 min), 2 readings, 2 quizzes
8 videos
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 Quiz20m
Module 4 Exam1h 10m
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Top reviews from Command Line Tools for Genomic Data Science

By JJJun 23rd 2018

Thank you very much Dr./Professor, Liliana Florea. I've learned a lot. It's a very good opportunity to improve my knowledge. This means a lot to me.

By GVMar 14th 2016

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



Liliana Florea, PhD

Assistant Professor
McKusick-Nathans Institute of Genetic Medicine

About 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....

About the Genomic Data Science Specialization

With genomics sparks a revolution in medical discoveries, it becomes imperative to be able to better understand the genome, and be able to leverage the data and information from genomic datasets. Genomic Data Science is the field that applies statistics and data science to the genome. This Specialization covers the concepts and tools to understand, analyze, and interpret data from next generation sequencing experiments. It teaches the most common tools used in genomic data science including how to use the command line, along with a variety of software implementation tools like Python, R, Bioconductor, and Galaxy. This Specialization is designed to serve as both a standalone introduction to genomic data science or as a perfect compliment to a primary degree or postdoc in biology, molecular biology, or genetics, for scientists in these fields seeking to gain familiarity in data science and statistical tools to better interact with the data in their everyday work. To audit Genomic Data Science courses for free, visit https://www.coursera.org/jhu, click the course, click Enroll, and select Audit. Please note that you will not receive a Certificate of Completion if you choose to Audit....
Genomic Data Science

Frequently Asked Questions

  • Once you enroll for a Certificate, you’ll have access to all videos, quizzes, and programming assignments (if applicable). Peer review assignments can only be submitted and reviewed once your session has begun. If you choose to explore the course without purchasing, you may not be able to access certain assignments.

  • 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.

More questions? Visit the Learner Help Center.