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Systematic comparison and assessment of RNA-seq procedures for gene expression quantitative analysis
Luis A Corchete1,2,3,4,5, Elizabeta A Rojas6,7,8, Diego Alonso-López7
1Hematology Department, University Hospital, 37007, Salamanca, Spain. lacorsan@usal.es.
Scientific Reports
|November 13, 2020
Summary
This study evaluates 192 RNA-seq analysis pipelines for gene expression and differential expression. It provides a guide to RNA sequencing data analysis methods, aiding researchers in selecting optimal algorithms for accurate results.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- RNA sequencing (RNA-seq) is a powerful tool for genome-wide gene expression analysis.
- The complexity of RNA-seq data analysis has led to numerous algorithms and pipelines.
- A lack of consensus exists regarding the optimal methods for RNA-seq data analysis.
Purpose of the Study:
- To evaluate the performance of various RNA-seq analysis pipelines.
- To provide a comprehensive guide to RNA-seq data analysis methods.
- To compare algorithms for raw gene expression quantification and differential gene expression analysis.
Main Methods:
- Applied 192 pipelines with alternative methods to 18 human cell line samples.
- Quantified raw gene expression signals using non-parametric statistics.
- Estimated differential gene expression performance using 17 different methods.
- Validated procedures using quantitative reverse transcription PCR (qRT-PCR).
Main Results:
- Evaluated the precision and accuracy of raw gene expression quantification.
- Assessed the performance of 17 differential gene expression methods.
- Identified advantages and disadvantages of tested algorithms and pipelines.
- Provided empirical validation through qRT-PCR.
Conclusions:
- The study offers a comparative analysis of RNA-seq data processing pipelines.
- It guides researchers in selecting appropriate methods for gene expression and differential expression analysis.
- Findings contribute to establishing best practices in RNA-seq data interpretation.
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