About this course: 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.
Created by: Johns Hopkins University
Taught by: Liliana Florea, PhD, Assistant Professor
McKusick-Nathans Institute of Genetic Medicine
| Basic Info | Course 5 of 8 in the Genomic Data Science Specialization |
| Language | English |
| How To Pass | Pass all graded assignments to complete the course. |
| User Ratings |
Syllabus
WEEK 1
Basic Unix Commands
In this module, you will be introduced to command Line Tools for Genomic Data Science
12 videos, 5 readings
- Reading: Welcome Message
- Reading: Syllabus
- Reading: VMBox Download & Instructions
- Reading: Pre-Course Survey
- Video: Basic Unix Commands 1: Content Representation
- Video: Basic Unix Commands 2: Files, Directories, Paths
- Video: Basic Unix Commands 3: File Naming
- Video: Basic Unix Commands 4: Content Creation
- Video: Basic Unix Commands 5: Accessing Content I
- Video: Basic Unix Commands 6: Accessing Content II
- Video: Basic Unix Commands 7: Redirecting Content
- Video: Basic Unix Commands 8: Querying Content
- Video: Basic Unix Commands 9: Comparing Content
- Video: Basic Unix Commands 10: Archiving Content
- Video: Basic Unix Commands 11: Practical Exercises I
- Video: Basic Unix Commands 12: Practical Exercises II
- Reading: Module 1 Exam Instructions **IMPORTANT**
Graded: Module 1 Quiz
Graded: Module 1 Exam
WEEK 2
Week Two
In this module, we'll be taking a look at Sequences and Genomic Features in a sequence of 10 presentations.
11 videos, 1 reading
- Video: Sequences and Genomic Features 1: Molecular Bio Primer
- Video: Sequences and Genomic Features 2: Sequence Representation and Generation
- Video: Sequences and Genomic Features 3: Annotation
- Video: Sequences and Genomic Features 4.1: Alignment I
- Video: Sequences and Genomic Features 4.2: Alignment II
- Video: Sequences and Genomic Features 5: Recreating Sequences & Features
- Video: Sequences and Genomic Features 6: Genomic Feature Retrieval
- Video: Sequences and Genomic Features 7: SAMtools I
- Video: Sequences and Genomic Features 8: SAMtools II
- Video: Sequences and Genomic Features 9: BEDtools I
- Video: Sequences and Genomic Features 10: BEDtools II
- Reading: Module 2 Exam Instructions **IMPORTANT**
Graded: Module 2 Quiz
Graded: Module 2 Exam
WEEK 3
Week Three
In this module, we'll be going over Alignment and Sequence Variation in another sequence of 8 presentations.
8 videos, 1 reading
- Video: Alignment & Sequence Variation 1: Overview
- Video: Alignment & Sequence Variation 2: Alignment & Variant Detection Tools
- Video: Alignment & Sequence Variation 3: VCF
- Video: Alignment & Sequence Variation 4: Bowtie
- Video: Alignment & Sequence Variation 5: BWA
- Video: Alignment & Sequence Variation 6: SAMtools (mpileup)
- Video: Alignment & Sequence Variation 7: BCFtools
- Video: Alignment & Sequence Variation 8: Variant Calling
- Reading: Module 3 Exam Instructions **IMPORTANT**
Graded: Module 3 Quiz
Graded: Module 3 Exam
WEEK 4
Week Four
In this module, we'll be going over Tools for Transcriptomics in a sequence of 6 presentations.
8 videos, 2 readings
- Video: Tools for Transcriptomics 1: Overview
- Video: Tools for Transcriptomics 2: RNA-seq
- Video: Tools for Transcriptomics 3.1: Tophat I
- Video: Tools for Transcriptomics 3.2: Tophat II
- Video: Tools for Transcriptomics 4: Cufflinks
- Video: Tools for Transcriptomics 5: Cuffdiff
- Video: Tools for Transcriptomics 6.1: Integrated Genomics Viewer I
- Video: Tools for Transcriptomics 6.2: Integrated Genomics Viewer II
- Reading: Module 4 Exam Instructions **IMPORTANT**
- Reading: Post-Course Survey
Graded: Module 4 Quiz
Graded: Module 4 Exam
FAQs
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Coursework
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Creators
Johns Hopkins University
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Pricing
| Audit | Purchase Course | |
|---|---|---|
| Access to course materials | Available | Available |
| Access to graded materials | Not available | Available |
| Receive a final grade | Not available | Available |
| Earn a shareable Course Certificate | Not available | Available |
Ratings and Reviews
Excellent quizzes and exams. Smooth flow of lectures. However, as a beginner I faced a lot of difficulty in installing the required tools. I could complete the course only because the tools were provided as a package with the VM box. I will be handling NGS data for my PhD project, for which I will have to install the latest versions of these tools. Manuals are cryptic. A lot of errors keep cropping up whenever I try to install anything. This course should have taught us that part too. I shall be thankful if you could provide a short course or a step by step write up for the same, else we will not be able to apply what such a good course taught us.
Simple, straight forward and descriptive
Great course. The last exam is a little bit tricky, specially when some commands are large and confusing. But with the help of forums, you can still find the right answers.
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the best course i have ever ever taken.