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.
本課程是 Genomic Data Science 專項課程 專項課程的一部分
Command Line Tools for Genomic Data Science
提供方
教學大綱 - 您將從這門課程中學到什麼
週
1Basic Unix Commands
In this module, you will be introduced to command Line Tools for Genomic Data Science
12 個視頻（共 105 分鐘）, 5 個閱讀材料, 2 個測驗
12 個視頻
Basic Unix Commands 2: Files, Directories, Paths7分鐘
Basic Unix Commands 3: File Naming4分鐘
Basic Unix Commands 4: Content Creation9分鐘
Basic Unix Commands 5: Accessing Content I6分鐘
Basic Unix Commands 6: Accessing Content II4分鐘
Basic Unix Commands 7: Redirecting Content6分鐘
Basic Unix Commands 8: Querying Content15分鐘
Basic Unix Commands 9: Comparing Content11分鐘
Basic Unix Commands 10: Archiving Content13分鐘
Basic Unix Commands 11: Practical Exercises I13分鐘
Basic Unix Commands 12: Practical Exercises II9分鐘
5 個閱讀材料
Welcome Message10分鐘
Syllabus10分鐘
VMBox Download & Instructions10分鐘
Pre-Course Survey10分鐘
Module 1 Exam Instructions **IMPORTANT**10分鐘
2 個練習
Module 1 Quiz20分鐘
Module 1 Exam34分鐘
週
2Week Two
In this module, we'll be taking a look at Sequences and Genomic Features in a sequence of 10 presentations.
11 個視頻（共 127 分鐘）, 1 個閱讀材料, 2 個測驗
11 個視頻
Sequences and Genomic Features 2: Sequence Representation and Generation11分鐘
Sequences and Genomic Features 3: Annotation14分鐘
Sequences and Genomic Features 4.1: Alignment I13分鐘
Sequences and Genomic Features 4.2: Alignment II9分鐘
Sequences and Genomic Features 5: Recreating Sequences & Features12分鐘
Sequences and Genomic Features 6: Genomic Feature Retrieval5分鐘
Sequences and Genomic Features 7: SAMtools I11分鐘
Sequences and Genomic Features 8: SAMtools II9分鐘
Sequences and Genomic Features 9: BEDtools I15分鐘
Sequences and Genomic Features 10: BEDtools II15分鐘
1 個閱讀材料
Module 2 Exam Instructions **IMPORTANT**10分鐘
2 個練習
Module 2 Quiz20分鐘
Module 2 Exam40分鐘
週
3Week Three
In this module, we'll be going over Alignment and Sequence Variation in another sequence of 8 presentations.
8 個視頻（共 55 分鐘）, 1 個閱讀材料, 2 個測驗
8 個視頻
Alignment & Sequence Variation 2: Alignment & Variant Detection Tools5分鐘
Alignment & Sequence Variation 3: VCF11分鐘
Alignment & Sequence Variation 4: Bowtie9分鐘
Alignment & Sequence Variation 5: BWA 4分鐘
Alignment & Sequence Variation 6: SAMtools (mpileup)6分鐘
Alignment & Sequence Variation 7: BCFtools8分鐘
Alignment & Sequence Variation 8: Variant Calling5分鐘
1 個閱讀材料
Module 3 Exam Instructions **IMPORTANT**10分鐘
2 個練習
Module 3 Quiz20分鐘
Module 3 Exam48分鐘
週
4Week Four
In this module, we'll be going over Tools for Transcriptomics in a sequence of 6 presentations.
8 個視頻（共 75 分鐘）, 2 個閱讀材料, 2 個測驗
8 個視頻
Tools for Transcriptomics 2: RNA-seq7分鐘
Tools for Transcriptomics 3.1: Tophat I9分鐘
Tools for Transcriptomics 3.2: Tophat II 8分鐘
Tools for Transcriptomics 4: Cufflinks10分鐘
Tools for Transcriptomics 5: Cuffdiff16分鐘
Tools for Transcriptomics 6.1: Integrated Genomics Viewer I8分鐘
Tools for Transcriptomics 6.2: Integrated Genomics Viewer II 6分鐘
2 個閱讀材料
Module 4 Exam Instructions **IMPORTANT**10分鐘
Post-Course Survey10分鐘
2 個練習
Module 4 Quiz20分鐘
Module 4 Exam10分鐘
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熱門審閱
創建者 JJ•Jun 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.
創建者 GV•Mar 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.
講師
Liliana Florea, PhD
Assistant ProfessorMcKusick-Nathans Institute of Genetic Medicine
關於 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.
關於 Genomic Data Science 專項課程
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, Python, R, Bioconductor, and Galaxy. The sequence is a stand alone introduction to genomic data science or a perfect compliment to a primary degree or postdoc in biology, molecular biology, or genetics.
To audit Genomic Data Science courses for free, visit https://www.coursera.org/jhu, click the course, click Enroll, and select Audit.
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