Command Line Tools for Genomic Data Science

Command Line Tools for Genomic Data Science

This course is part of Genomic Data Science Specialization

Instructor: Liliana Florea, PhD

Skills you'll gain

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Assessments

8 assignments

Taught in English

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This course is part of the Genomic Data Science Specialization

When you enroll in this course, you'll also be enrolled in this Specialization.

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There are 4 modules in this course

In this module, you will be introduced to Command Line Tools for Genomic Data Science

What's included

12 videos6 readings2 assignments

12 videosTotal 105 minutes

Basic Unix Commands 1: Content Representation3 minutesPreview module
Basic Unix Commands 2: Files, Directories, Paths7 minutes
Basic Unix Commands 3: File Naming4 minutes
Basic Unix Commands 4: Content Creation9 minutes
Basic Unix Commands 5: Accessing Content I6 minutes
Basic Unix Commands 6: Accessing Content II4 minutes
Basic Unix Commands 7: Redirecting Content6 minutes
Basic Unix Commands 8: Querying Content15 minutes
Basic Unix Commands 9: Comparing Content11 minutes
Basic Unix Commands 10: Archiving Content13 minutes
Basic Unix Commands 11: Practical Exercises I13 minutes
Basic Unix Commands 12: Practical Exercises II9 minutes

6 readingsTotal 60 minutes

Welcome Message10 minutes
Syllabus10 minutes
VMBox Download & Instructions10 minutes
Docker Image Download & Instructions10 minutes
Pre-Course Survey10 minutes
Module 1 Exam Instructions **IMPORTANT**10 minutes

2 assignmentsTotal 60 minutes

Module 1 Quiz30 minutes
Module 1 Exam30 minutes

In this module, we'll be taking a look at Sequences and Genomic Features in a sequence of 10 presentations.

What's included

11 videos1 reading2 assignments

11 videosTotal 126 minutes

Sequences and Genomic Features 1: Molecular Bio Primer6 minutesPreview module
Sequences and Genomic Features 2: Sequence Representation and Generation11 minutes
Sequences and Genomic Features 3: Annotation14 minutes
Sequences and Genomic Features 4.1: Alignment I13 minutes
Sequences and Genomic Features 4.2: Alignment II9 minutes
Sequences and Genomic Features 5: Recreating Sequences & Features12 minutes
Sequences and Genomic Features 6: Genomic Feature Retrieval5 minutes
Sequences and Genomic Features 7: SAMtools I11 minutes
Sequences and Genomic Features 8: SAMtools II9 minutes
Sequences and Genomic Features 9: BEDtools I15 minutes
Sequences and Genomic Features 10: BEDtools II15 minutes

1 readingTotal 10 minutes

Module 2 Exam Instructions **IMPORTANT**10 minutes

2 assignmentsTotal 60 minutes

Module 2 Quiz30 minutes
Module 2 Exam30 minutes

In this module, we'll be going over Alignment and Sequence Variation in another sequence of 8 presentations.

What's included

8 videos1 reading2 assignments

8 videosTotal 54 minutes

Alignment & Sequence Variation 1: Overview4 minutesPreview module
Alignment & Sequence Variation 2: Alignment & Variant Detection Tools5 minutes
Alignment & Sequence Variation 3: VCF11 minutes
Alignment & Sequence Variation 4: Bowtie9 minutes
Alignment & Sequence Variation 5: BWA 4 minutes
Alignment & Sequence Variation 6: SAMtools (mpileup)6 minutes
Alignment & Sequence Variation 7: BCFtools8 minutes
Alignment & Sequence Variation 8: Variant Calling5 minutes

1 readingTotal 10 minutes

Module 3 Exam Instructions **IMPORTANT**10 minutes

2 assignmentsTotal 60 minutes

Module 3 Quiz30 minutes
Module 3 Exam30 minutes

In this module, we'll be going over Tools for Transcriptomics in a sequence of 6 presentations.

What's included

8 videos2 readings2 assignments

8 videosTotal 74 minutes

Tools for Transcriptomics 1: Overview6 minutesPreview module
Tools for Transcriptomics 2: RNA-seq7 minutes
Tools for Transcriptomics 3.1: Tophat I9 minutes
Tools for Transcriptomics 3.2: Tophat II 8 minutes
Tools for Transcriptomics 4: Cufflinks10 minutes
Tools for Transcriptomics 5: Cuffdiff16 minutes
Tools for Transcriptomics 6.1: Integrated Genomics Viewer I8 minutes
Tools for Transcriptomics 6.2: Integrated Genomics Viewer II 6 minutes

2 readingsTotal 20 minutes

Module 4 Exam Instructions **IMPORTANT**10 minutes
Post-Course Survey10 minutes

2 assignmentsTotal 60 minutes

Module 4 Quiz30 minutes
Module 4 Exam30 minutes

Instructor

Instructor ratings

3.4 (55 ratings)

Liliana Florea, PhD

Johns Hopkins University

2 Courses30,103 learners

Offered by

Johns Hopkins University

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Reviewed on Jun 26, 2020

A very well planned course for beginners who don't have any experience with command line language for exploring genomic data

Reviewed on Aug 28, 2017

Highly recommended.

Reviewed on Mar 10, 2022

Course explanation is good but some topics are not updated like mplieup is now not included in samtools and they didnot update information. Instructor taught lectures very well.

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