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.
Este curso forma parte de Programa Especializado - Genomic Data Science
Command Line Tools for Genomic Data Science
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Acerca de este Curso
19,193 vistas recientes
Habilidades que obtendrás
BioinformaticsSamtoolsUnixCommand-Line Interface
Programa - Qué aprenderás en este curso
Semana
13 horas para completar
Basic Unix Commands
In this module, you will be introduced to command Line Tools for Genomic Data Science
12 videos (Total 105 minutos), 5 readings, 2 quizzes
12 videos
Basic Unix Commands 2: Files, Directories, Paths7m
Basic Unix Commands 3: File Naming4m
Basic Unix Commands 4: Content Creation9m
Basic Unix Commands 5: Accessing Content I6m
Basic Unix Commands 6: Accessing Content II4m
Basic Unix Commands 7: Redirecting Content6m
Basic Unix Commands 8: Querying Content15m
Basic Unix Commands 9: Comparing Content11m
Basic Unix Commands 10: Archiving Content13m
Basic Unix Commands 11: Practical Exercises I13m
Basic Unix Commands 12: Practical Exercises II9m
5 lecturas
Welcome Message10m
Syllabus10m
VMBox Download & Instructions10m
Pre-Course Survey10m
Module 1 Exam Instructions **IMPORTANT**10m
2 ejercicios de práctica
Module 1 Quiz20m
Module 1 Exam34m
Semana
23 horas para completar
Week Two
In this module, we'll be taking a look at Sequences and Genomic Features in a sequence of 10 presentations.
11 videos (Total 127 minutos), 1 reading, 2 quizzes
11 videos
Sequences and Genomic Features 2: Sequence Representation and Generation11m
Sequences and Genomic Features 3: Annotation14m
Sequences and Genomic Features 4.1: Alignment I13m
Sequences and Genomic Features 4.2: Alignment II9m
Sequences and Genomic Features 5: Recreating Sequences & Features12m
Sequences and Genomic Features 6: Genomic Feature Retrieval5m
Sequences and Genomic Features 7: SAMtools I11m
Sequences and Genomic Features 8: SAMtools II9m
Sequences and Genomic Features 9: BEDtools I15m
Sequences and Genomic Features 10: BEDtools II15m
1 lectura
Module 2 Exam Instructions **IMPORTANT**10m
2 ejercicios de práctica
Module 2 Quiz20m
Module 2 Exam40m
Semana
32 horas para completar
Week Three
In this module, we'll be going over Alignment and Sequence Variation in another sequence of 8 presentations.
8 videos (Total 55 minutos), 1 reading, 2 quizzes
8 videos
Alignment & Sequence Variation 2: Alignment & Variant Detection Tools5m
Alignment & Sequence Variation 3: VCF11m
Alignment & Sequence Variation 4: Bowtie9m
Alignment & Sequence Variation 5: BWA 4m
Alignment & Sequence Variation 6: SAMtools (mpileup)6m
Alignment & Sequence Variation 7: BCFtools8m
Alignment & Sequence Variation 8: Variant Calling5m
1 lectura
Module 3 Exam Instructions **IMPORTANT**10m
2 ejercicios de práctica
Module 3 Quiz20m
Module 3 Exam48m
Semana
43 horas para completar
Week Four
In this module, we'll be going over Tools for Transcriptomics in a sequence of 6 presentations.
8 videos (Total 75 minutos), 2 readings, 2 quizzes
8 videos
Tools for Transcriptomics 2: RNA-seq7m
Tools for Transcriptomics 3.1: Tophat I9m
Tools for Transcriptomics 3.2: Tophat II 8m
Tools for Transcriptomics 4: Cufflinks10m
Tools for Transcriptomics 5: Cuffdiff16m
Tools for Transcriptomics 6.1: Integrated Genomics Viewer I8m
Tools for Transcriptomics 6.2: Integrated Genomics Viewer II 6m
2 lecturas
Module 4 Exam Instructions **IMPORTANT**10m
Post-Course Survey10m
2 ejercicios de práctica
Module 4 Quiz20m
Module 4 Exam1h 10m
50%
comenzó una nueva carrera después de completar estos cursos
43%
consiguió un beneficio tangible en su carrera profesional gracias a este curso
20%
consiguió un aumento de sueldo o ascenso
Principales revisiones sobre Command Line Tools for Genomic Data Science
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.
Instructor
Liliana Florea, PhD
Assistant ProfessorMcKusick-Nathans Institute of Genetic Medicine
Acerca de Universidad Johns Hopkins
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.
Acerca del programa especializado Genomic Data Science
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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