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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Genomic Data Science SpecializationJohns Hopkins UniversityAbout this Course
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Learner Career Outcomes
50%
started a new career after completing these courses
43%
got a tangible career benefit from this course
20%
got a pay increase or promotion
Shareable Certificate
Earn a Certificate upon completion
100% online
Start instantly and learn at your own schedule.
Course 5 of 8 in the
Flexible deadlines
Reset deadlines in accordance to your schedule.
Approx. 12 hours to complete
English
Subtitles: English
Skills you will gain
BioinformaticsSamtoolsUnixCommand-Line Interface
Learner Career Outcomes
50%
started a new career after completing these courses
43%
got a tangible career benefit from this course
20%
got a pay increase or promotion
Shareable Certificate
Earn a Certificate upon completion
100% online
Start instantly and learn at your own schedule.
Course 5 of 8 in the
Flexible deadlines
Reset deadlines in accordance to your schedule.
Approx. 12 hours to complete
English
Subtitles: English
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
3 hours to complete
Basic Unix Commands
In this module, you will be introduced to command Line Tools for Genomic Data Science
3 hours to complete
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
Syllabus10m
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
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 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
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 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
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 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
Reviews
TOP REVIEWS FROM COMMAND LINE TOOLS FOR GENOMIC DATA SCIENCE
by SCOct 17, 2016
Th lecturer could be a little more engaging and the materials used during classes, if made available would help following it better, by replicating the examples being shown.
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
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 JJJun 22, 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.
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.
Frequently Asked Questions
When will I have access to the lectures and assignments?
Access to lectures and assignments depends on your type of enrollment. If you take a course in audit mode, you will be able to see most course materials for free. To access graded assignments and to earn a Certificate, you will need to purchase the Certificate experience, during or after your audit. If you don't see the audit option:
- The course may not offer an audit option. You can try a Free Trial instead, or apply for Financial Aid.
- The course may offer 'Full Course, No Certificate' instead. This option lets you see all course materials, submit required assessments, and get a final grade. This also means that you will not be able to purchase a Certificate experience.
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.
What is the refund policy?
If you subscribed, you get a 7-day free trial during which you can cancel at no penalty. After that, we don’t give refunds, but you can cancel your subscription at any time. See our full refund policy.
Is financial aid available?
Yes, Coursera provides financial aid to learners who cannot afford the fee. Apply for it by clicking on the Financial Aid link beneath the "Enroll" button on the left. You'll be prompted to complete an application and will be notified if you are approved. You'll need to complete this step for each course in the Specialization, including the Capstone Project. Learn more.
Will I earn university credit for completing the Course?
This Course doesn't carry university credit, but some universities may choose to accept Course Certificates for credit. Check with your institution to learn more. Online Degrees and Mastertrack™ Certificates on Coursera provide the opportunity to earn university credit.
More questions? Visit the Learner Help Center.
