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Guide to RNA-seq Analysis
  • Introduction
  • Preparations
    • Work environment
    • Softwares and databases
    • Obtain sequencing data
    • R packages
  • Raw read processing
    • QC & trimming
    • Mapping & quantification
      • Alignment-free method
      • Alignment-based method
  • Differential expression analysis in R
    • Building a TxDb object
    • About tximport
    • Convert Salmon output to Sleuth-compatible format
    • Differential gene expression (DGE) analysis using DESeq2
      • DGE analysis with Salmon/Kallisto input
      • DGE analysis with STAR input
      • DGE analysis with STAR + RSEM input
    • Differential transcript expression (DTE) analysis using DESeq2
      • DTE analysis with Salmon/Kallisto input
      • DTE analysis with STAR + RSEM input
    • DGE and DTE analysis of Salmon/Kallisto inputs using Sleuth
    • Differential transcript usage (DTU) analysis
      • DTU analysis using DRIMSeq
      • DTU analysis using DEXSeq
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  • We will perform DGE in the following directory
  • DGE analysis with following quantification inputs

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  1. Differential expression analysis in R

Differential gene expression (DGE) analysis using DESeq2

We will perform DGE in the following directory

cd /home/USER/SSAPs
mkdir analysis
mkdir analysis/dge
cd analysis/dge
R

DGE analysis with following quantification inputs

  • Salmon/Kallisto

  • STAR

  • STAR + RSEM

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Last updated 5 years ago

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