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Related Experiment Video

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Methods to Discover Alternative Promoter Usage and Transcriptional Regulation of Murine Bcrp1
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Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification.

Michael I Love1,2, Charlotte Soneson3,4, Rob Patro5

  • 1Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27516, USA.

F1000Research
|October 30, 2018
PubMed
Summary

This study introduces a fast R/Bioconductor workflow for detecting differential transcript usage (DTU) from RNA-seq data. The pipeline efficiently analyzes transcript-level expression using Salmon, DRIMSeq, DEXSeq, and stageR for robust DTU discovery.

Keywords:
DEXSeqDRIMSeqRNA-seqSalmondifferential transcript usagestageRtximportworkflow

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Differential transcript usage (DTU) analysis complements gene expression studies.
  • Existing methods for DTU detection can be computationally intensive.

Purpose of the Study:

  • To present a simple, fast, and efficient workflow for DTU detection using R/Bioconductor packages.
  • To integrate transcript-level quantification from Salmon with downstream DTU analysis tools.

Main Methods:

  • Utilized Salmon for transcript-level quantification of RNA-seq data.
  • Employed DRIMSeq and DEXSeq for DTU analysis.
  • Implemented a two-stage testing approach using the stageR package for gene and transcript-level screening.
  • Evaluated the workflow on a simulated dataset.

Main Results:

  • The proposed workflow is fast and efficient, leveraging Salmon's inference capabilities.
  • The stageR package enables effective screening and confirmation of DTU.
  • The workflow successfully integrates existing R/Bioconductor packages for a comprehensive DTU analysis.

Conclusions:

  • The presented workflow provides a streamlined approach for DTU detection from RNA-seq data.
  • This method facilitates the complementary analysis of gene expression and transcript usage.
  • The R/Bioconductor-based pipeline offers a robust and accessible tool for researchers.