Gene-level RNA-Seq Data Analysis (lagacy)
  • Introduction
  • RNA-Seq Analysis Workflow
    • Login to server
    • Obtain data and software
    • Create mapping indices
    • Mapping with STAR
    • Quantification using RSEM
  • De novo assembly using Trinity
    • De novo assembly of RNA-Seq reads
    • Compare de novo reconstructed transcripts to reference annotations
    • Quantification using RSEM
  • Differential expression analysis using R
    • Install R libraries
    • Perform DE analysis
    • Perform DE analysis (Trinity)
    • Extracting DE transcripts and generating heatmaps (Trinity)
  • Visualization
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  • Hands-on Training in RNA-Seq Data Analysis
  • History
  • License

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Introduction

NextRNA-Seq Analysis Workflow

Last updated 4 years ago

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Hands-on Training in RNA-Seq Data Analysis

I-Hsuan Lin

National Yang-Ming University, Taipei, Taiwan

The materials were prepared for the Next-Generation Sequencing Workshop organized by the Life Science Library Training Courses on 19th Nov 2015 at Academia Sinica.

As the title suggests, RNA-Seq (RNA sequencing) utilizes the next-generation technology to assay the presence and quantity of RNA molecules in the given sample. RNA-Seq offers many advantages and supersede the microarray technology that was introduced in 2000s. This includes detects known and novel transcripts, increased specificity and sensitivity, and identification of low-abundance transcripts and isoforms with sufficient sequencing depth. RNA-seq has also been used to discover alternative splicing variants, chimeric RNAs result from fusion genes and RNA editing sites.

History

Update (May 2020) New step-by-step guide available

Update: (Apr 2020) Migrate to the new Gitbook site, broken links/images fixed

Update: (Oct-Nov 2016) Mapping and analysis of the example datasets were re-ran with latest versions of the tools

License

Unless specified, this content is licensed under the Creative Commons — Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0). You may view a copy of this license at

here
https://creativecommons.org/licenses/by-nc-sa/4.0/
National Research Program for Biopharmaceuticals
National Yang-Ming University