📄
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
Powered by GitBook
On this page
  • We will perform DTE in the following directory
  • DTE analysis with following quantification inputs

Was this helpful?

  1. Differential expression analysis in R

Differential transcript expression (DTE) analysis using DESeq2

We will perform DTE in the following directory

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

DTE analysis with following quantification inputs

  • Salmon/Kallisto

  • STAR + RSEM

PreviousDGE analysis with STAR + RSEM inputNextDTE analysis with Salmon/Kallisto input

Last updated 5 years ago

Was this helpful?