Command Line Tools for Genomic Data Science
- 4.1
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Approx. 12 hours to complete
Course Summary
This course teaches you the fundamentals of genomic tools and the computational analysis of DNA sequences. You'll learn how to manipulate and analyze DNA sequences using various tools and techniques.Key Learning Points
- Learn the basics of genomics and DNA sequencing
- Understand how to use various tools like BLAST, Bowtie, and BWA
- Learn how to analyze genomic data using R
Related Topics for further study
Learning Outcomes
- Understand the basics of genomics and DNA sequencing
- Be proficient in using various genomic tools and techniques
- Be able to analyze genomic data using R
Prerequisites or good to have knowledge before taking this course
- Basic knowledge of biology and genetics
- Basic programming knowledge
Course Difficulty Level
IntermediateCourse Format
- Online self-paced
- Video lectures
- Assignments
Similar Courses
- Introduction to Genetics and Evolution
- Bioinformatics Specialization
Related Education Paths
Notable People in This Field
- Ewan Birney
- Neil Saunders
Related Books
Description
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.
Outline
- Basic Unix Commands
- Basic Unix Commands 1: Content Representation
- Basic Unix Commands 2: Files, Directories, Paths
- Basic Unix Commands 3: File Naming
- Basic Unix Commands 4: Content Creation
- Basic Unix Commands 5: Accessing Content I
- Basic Unix Commands 6: Accessing Content II
- Basic Unix Commands 7: Redirecting Content
- Basic Unix Commands 8: Querying Content
- Basic Unix Commands 9: Comparing Content
- Basic Unix Commands 10: Archiving Content
- Basic Unix Commands 11: Practical Exercises I
- Basic Unix Commands 12: Practical Exercises II
- Welcome Message
- Syllabus
- VMBox Download & Instructions
- Pre-Course Survey
- Module 1 Exam Instructions **IMPORTANT**
- Module 1 Quiz
- Module 1 Exam
- Week Two
- Sequences and Genomic Features 1: Molecular Bio Primer
- Sequences and Genomic Features 2: Sequence Representation and Generation
- Sequences and Genomic Features 3: Annotation
- Sequences and Genomic Features 4.1: Alignment I
- Sequences and Genomic Features 4.2: Alignment II
- Sequences and Genomic Features 5: Recreating Sequences & Features
- Sequences and Genomic Features 6: Genomic Feature Retrieval
- Sequences and Genomic Features 7: SAMtools I
- Sequences and Genomic Features 8: SAMtools II
- Sequences and Genomic Features 9: BEDtools I
- Sequences and Genomic Features 10: BEDtools II
- Module 2 Exam Instructions **IMPORTANT**
- Module 2 Quiz
- Module 2 Exam
- Week Three
- Alignment & Sequence Variation 1: Overview
- Alignment & Sequence Variation 2: Alignment & Variant Detection Tools
- Alignment & Sequence Variation 3: VCF
- Alignment & Sequence Variation 4: Bowtie
- Alignment & Sequence Variation 5: BWA
- Alignment & Sequence Variation 6: SAMtools (mpileup)
- Alignment & Sequence Variation 7: BCFtools
- Alignment & Sequence Variation 8: Variant Calling
- Module 3 Exam Instructions **IMPORTANT**
- Module 3 Quiz
- Module 3 Exam
- Week Four
- Tools for Transcriptomics 1: Overview
- Tools for Transcriptomics 2: RNA-seq
- Tools for Transcriptomics 3.1: Tophat I
- Tools for Transcriptomics 3.2: Tophat II
- Tools for Transcriptomics 4: Cufflinks
- Tools for Transcriptomics 5: Cuffdiff
- Tools for Transcriptomics 6.1: Integrated Genomics Viewer I
- Tools for Transcriptomics 6.2: Integrated Genomics Viewer II
- Module 4 Exam Instructions **IMPORTANT**
- Post-Course Survey
- Module 4 Quiz
- Module 4 Exam
Summary of User Reviews
Discover the power of genomic tools through this Coursera course. Students praise the thoroughness of the content and its applicability to real-world scenarios.Key Aspect Users Liked About This Course
Thoroughness and applicability of contentPros from User Reviews
- In-depth coverage of genomic tools and applications
- Real-world examples make the content more relatable
- Well-structured course with clear explanations
- Engaging and knowledgeable instructors
- Great value for the price
Cons from User Reviews
- Some technical jargon may be difficult for beginners to understand
- Requires a solid foundation in biology and genetics
- Can be time-consuming, especially for those with busy schedules
- Limited opportunity for interaction with instructors and peers
- No hands-on exercises or laboratory work
Liliana Florea, PhD
4.1 Raiting
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