À propos de ce cours : 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.
Créé par : Université Johns-Hopkins
Enseigné par : Liliana Florea, PhD, Assistant Professor
McKusick-Nathans Institute of Genetic Medicine
| Informations de base | Cours 5 de 8 dans Genomic Data Science Specialization |
| Langue | English |
| Comment réussir | Réussissez tous les devoirs notés pour terminer le cours. |
| Notes des utilisateurs |
Programme de cours
SEMAINE 1
Basic Unix Commands
In this module, you will be introduced to command Line Tools for Genomic Data Science
12 vidéos, 5 lectures
- Reading: Welcome Message
- Reading: Syllabus
- Reading: VMBox Download & Instructions
- Reading: Pre-Course Survey
- Vidéo: Basic Unix Commands 1: Content Representation
- Vidéo: Basic Unix Commands 2: Files, Directories, Paths
- Vidéo: Basic Unix Commands 3: File Naming
- Vidéo: Basic Unix Commands 4: Content Creation
- Vidéo: Basic Unix Commands 5: Accessing Content I
- Vidéo: Basic Unix Commands 6: Accessing Content II
- Vidéo: Basic Unix Commands 7: Redirecting Content
- Vidéo: Basic Unix Commands 8: Querying Content
- Vidéo: Basic Unix Commands 9: Comparing Content
- Vidéo: Basic Unix Commands 10: Archiving Content
- Vidéo: Basic Unix Commands 11: Practical Exercises I
- Vidéo: Basic Unix Commands 12: Practical Exercises II
- Reading: Module 1 Exam Instructions **IMPORTANT**
Noté: Module 1 Quiz
Noté: Module 1 Exam
SEMAINE 2
Week Two
In this module, we'll be taking a look at Sequences and Genomic Features in a sequence of 10 presentations.
11 vidéos, 1 lecture
- Vidéo: Sequences and Genomic Features 1: Molecular Bio Primer
- Vidéo: Sequences and Genomic Features 2: Sequence Representation and Generation
- Vidéo: Sequences and Genomic Features 3: Annotation
- Vidéo: Sequences and Genomic Features 4.1: Alignment I
- Vidéo: Sequences and Genomic Features 4.2: Alignment II
- Vidéo: Sequences and Genomic Features 5: Recreating Sequences & Features
- Vidéo: Sequences and Genomic Features 6: Genomic Feature Retrieval
- Vidéo: Sequences and Genomic Features 7: SAMtools I
- Vidéo: Sequences and Genomic Features 8: SAMtools II
- Vidéo: Sequences and Genomic Features 9: BEDtools I
- Vidéo: Sequences and Genomic Features 10: BEDtools II
- Reading: Module 2 Exam Instructions **IMPORTANT**
Noté: Module 2 Quiz
Noté: Module 2 Exam
SEMAINE 3
Week Three
In this module, we'll be going over Alignment and Sequence Variation in another sequence of 8 presentations.
8 vidéos, 1 lecture
- Vidéo: Alignment & Sequence Variation 1: Overview
- Vidéo: Alignment & Sequence Variation 2: Alignment & Variant Detection Tools
- Vidéo: Alignment & Sequence Variation 3: VCF
- Vidéo: Alignment & Sequence Variation 4: Bowtie
- Vidéo: Alignment & Sequence Variation 5: BWA
- Vidéo: Alignment & Sequence Variation 6: SAMtools (mpileup)
- Vidéo: Alignment & Sequence Variation 7: BCFtools
- Vidéo: Alignment & Sequence Variation 8: Variant Calling
- Reading: Module 3 Exam Instructions **IMPORTANT**
Noté: Module 3 Quiz
Noté: Module 3 Exam
SEMAINE 4
Week Four
In this module, we'll be going over Tools for Transcriptomics in a sequence of 6 presentations.
8 vidéos, 2 lectures
- Vidéo: Tools for Transcriptomics 1: Overview
- Vidéo: Tools for Transcriptomics 2: RNA-seq
- Vidéo: Tools for Transcriptomics 3.1: Tophat I
- Vidéo: Tools for Transcriptomics 3.2: Tophat II
- Vidéo: Tools for Transcriptomics 4: Cufflinks
- Vidéo: Tools for Transcriptomics 5: Cuffdiff
- Vidéo: Tools for Transcriptomics 6.1: Integrated Genomics Viewer I
- Vidéo: Tools for Transcriptomics 6.2: Integrated Genomics Viewer II
- Reading: Module 4 Exam Instructions **IMPORTANT**
- Reading: Post-Course Survey
Noté: Module 4 Quiz
Noté: Module 4 Exam
FAQ
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Créateurs
Université 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.
Tarification
| Acheter le cours | |
|---|---|
| Accéder au contenu du cours | Disponible |
| Accéder au contenu noté | Disponible |
| Recevoir une Note Finale | Disponible |
| Obtenir un Certificat de Cours partageable | Disponible |
Notation et examens
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