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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Pricing
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| Access to course materials | Available |
| Access to graded materials | Available |
| Receive a final grade | Available |
| Earn a shareable Course Certificate | Available |
Ratings and Reviews
A really hard introduction to bioinformatics pipelines, it was difficult but was stimulant!
This was one of the most valuable courses I have taken online.
Thank you
Great course. I think it should be the first in the whole series.
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EL
Clear, very practical and applicable