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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RNA-Seq Analysis Workflow

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Last updated 5 years ago

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Below shows a general workflow for carrying out a RNA-Seq experiment. In this guide, I will focus on the pre-processing of NGS raw reads, mapping, quantification and identification of differentially expressed genes and transcripts.

Workflow