Course

Command Line Tools for Genomic Data Science

Johns Hopkins University

Embark on a transformative journey with the Command Line Tools for Genomic Data Science course. This specialized program delves into the essential commands required for efficient management and analysis of directories, files, and extensive genomic data. Through a series of engaging modules, students gain proficiency in utilizing Unix commands, exploring sequences and genomic features, understanding alignment and sequence variation, and mastering tools for transcriptomics.

Developed by Johns Hopkins University, this course empowers learners to navigate the complexities of genomic data science, enabling them to make meaningful contributions to the field. Participants will benefit from interactive learning experiences, hands-on exercises, and comprehensive assessments that solidify their understanding of genomic data management and analysis.

Gain proficiency in managing and analyzing directories, files, and large sets of genomic data
Explore Unix commands and their applications in genomic data science
Understand sequences, genomic features, alignment, and sequence variation
Master tools for transcriptomics and their significance in genomic data analysis

Certificate Available ✔

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Command Line Tools for Genomic Data Science

This course comprises four comprehensive modules that cover Unix commands, sequences and genomic features, alignment and sequence variation, and tools for transcriptomics, providing learners with a holistic understanding of managing and analyzing genomic data.

Basic Unix Commands

Module 1: Basic Unix Commands

Master fundamental Unix commands for content representation, file management, and data access
Engage in practical exercises to reinforce learning
Complete an exam and quiz to assess your understanding of basic Unix commands

Week Two

Module 2: Sequences and Genomic Features

Explore molecular biology primer, sequence representation, and genomic feature retrieval
Learn about alignment, SAMtools, and BEDtools for genomic data analysis
Participate in an exam and quiz to test your knowledge of sequences and genomic features

Week Three

Module 3: Alignment & Sequence Variation

Gain insights into alignment, variant detection tools, and Variant Call Format (VCF)
Understand the significance of tools such as Bowtie, BWA, and SAMtools in genomic data analysis
Assess your understanding through an exam and quiz focusing on alignment and sequence variation

Week Four

Module 4: Tools for Transcriptomics

Delve into RNA-seq, Tophat, Cufflinks, and Cuffdiff for transcriptomic analysis
Learn to utilize Integrated Genomics Viewer for comprehensive analysis of transcriptomic data
Participate in a post-course survey, quiz, and exam to evaluate your grasp of transcriptomic tools and techniques

Course

Command Line Tools for Genomic Data Science

Course Modules

Basic Unix Commands

Week Two

Week Three

Week Four

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