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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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  1. Differential expression analysis in R

Differential transcript usage (DTU) analysis

PreviousDGE and DTE analysis of Salmon/Kallisto inputs using SleuthNextDTU analysis using DRIMSeq

Last updated 5 years ago

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We will perform DTU in the following directory

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

The proposed workflow is adapted from the a 2018 publication authored by .

We will use the quantification data generated by Salmon to perform DTU detection by the statistical methods, DRIMSeq and DEXSeq. As proposed in the paper, we will also use stageR to further control the overall false discovery rate (OFDR) across genes and transcripts

Michael Love, et al. in F1000Res
DTU analysis using DRIMSeq
DTU analysis using DEXSeq