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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課程信息
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您將獲得的技能
BioinformaticsSamtoolsUnixCommand-Line Interface
學習Course的學生是
- Biologists
- Biostatisticians
- Scientists
- Researchers
- Data Scientists
教學大綱 - 您將從這門課程中學到什麼
週
1完成時間為 3 小時
Basic Unix Commands
In this module, you will be introduced to command Line Tools for Genomic Data Science
12 個視頻 （總計 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
2完成時間為 3 小時
Week 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 （總計 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
3完成時間為 2 小時
Week Three
In this module, we'll be going over Alignment and Sequence Variation in another sequence of 8 presentations.
8 個視頻 （總計 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
4完成時間為 3 小時
Week Four
In this module, we'll be going over Tools for Transcriptomics in a sequence of 6 presentations.
8 個視頻 （總計 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 Exam1 小時 10 分
4.2
84 個審閱50%
完成這些課程後已開始新的職業生涯
43%
通過此課程獲得實實在在的工作福利
20%
加薪或升職
來自用于基因组数据科学的命令行工具的熱門評論
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.
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 约翰霍普金斯大学
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 基因组数据科学 專項課程
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.
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