Introduction to RNA-Seq: Leptin expression in mouse

Submission Details

Submission Date	December, 2019
Version	1.0
Authors	Jason Williams, Cold Spring Harbor Laboratory Judy Brusslan, California State University Long Beach Ray Enke, Jame Madison University Matthew Escobar, California State University San Marcos Vince Buonaccorsi, Juaniata College
Corresponding author	Jason Williams (williams@cshl.edu)

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Lesson Overview

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Learning Topics

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Student Prerequisites

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Instructor Prerequisites

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Accessibility

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Table of Contents

• Lesson home
• Launch Lesson on CyVerse
  • Get a CyVerse Account
  • Launch a lesson on CyVerse
  • Data Management on CyVerse
  • Backup Notebook
• Jupyter Primer
  • Intro to Jupyter and JupyterLab
  • Navigate Jupyter Lab
  • Using the Launcher to Run and Edit Jupyter Notebooks
  • Notebook Tips
  • Using the Bash Terminal in Jupyter Lab
• Command Line Primer
  • Command Line Intro
  • Command Line Syntax
  • Command Glossary
  • More Command Line Syntax Tips
  • Long Commands and Loops
• Intro to RNA-Seq
  • RNA-Seq - A look into the transcriptome
  • RNA-Seq Experiment
  • Example Experiment: Leptin expression in mouse tumor
  • Using This Lesson
    • Working with Notebooks
  • Questions
• Getting Data from NCBI
  • NCBI Sequence Read Archive
  • Accessing an SRA Bioproject
    • Exercise: searching on SRA
  • Downloading and converting data from SRA
  • Questions
• Assessing Data Quality
  • Introduction to FastQ files
  • FastQ file format
  • Phred score in detail
  • Running and interpreting FastQC
  • Running FastQC
  • Questions
• Trimming and Filtering Data
  • Filtering and trimming of data
  • Trimmomatic Functionalities
  • Use Trimmomatic to trim and filter RNA-Seq reads
  • Questions
• Pseudoalignment of Data Using Kallisto
  • The Ideal RNA-Seq experiment
  • Real-world RNA-Seq
  • RNA-Seq with Kallisto
  • Pseudoalignment and genomics word search
  • Use Kallisto to Pseudoalign RNA-Seq Reads
  • Questions
• Visualization of Aligned Data
  • Visualization of RNA-Seq Data
  • Visualization tools
  • Use Genome Browsers to Visualize RNA-Seq Reads
  • Questions
• Summary and Conclusion
  • Saving your work