RNA-seq Sample Preparation Kits Strongly Affect Transcriptome Profiles of a Gas-Fermenting Bacterium

Lima, Lorena Azevedo de; Reinmets, Kristina; Nielsen, Lars K.; Marcellin, Esteban; Harris, Audrey; Köpke, Michael; Valgepea, Kaspar

doi:10.1128/spectrum.02303-22

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Microbiol Spectr

2022

DOI: 10.1128/spectrum.02303-22

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RNA-seq Sample Preparation Kits Strongly Affect Transcriptome Profiles of a Gas-Fermenting Bacterium

Lorena Azevedo de Lima

Kristina Reinmets

Lars K. Nielsen

et al.

Abstract: RNA-seq is a powerful technique for transcriptome profiling while involving elaborate sample processing before library sequencing. We show that RNA-seq library preparation kits can strongly affect the outcome of an RNA-seq experiment.

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2023

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FASTdRNA: a workflow for the analysis of ONT direct RNA sequencing

Chen¹,

Liu²,

Lv³

et al. 2023

Bioinformatics Advances

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Motivation Direct RNA-seq (dRNA-seq) using Oxford Nanopore Technology (ONT) has revolutionized transcript mapping by offering enhanced precision due to its long read length. Unlike traditional techniques, dRNA-seq eliminates the need for PCR amplification, reducing the impact of GC bias and preserving valuable base physical information, such as RNA modification and poly(A) length estimation. However, the rapid advancement of ONT devices has set higher standards for analytical software, resulting in potential challenges of software incompatibility and reduced efficiency. Results We present a novel workflow, called FASTdRNA, to manipulate direct RNA-seq data efficiently. This workflow comprises two modules: a data preprocessing module and a data analysis module. The preprocessing data module, dRNAmain, encompasses basecalling, mapping, and transcript counting, which are essential for subsequent analyses. The data analysis module consists of a range of downstream analyses that facilitate the estimation of poly(A) length, prediction of RNA modifications, and assessment of alternative splicing events across different conditions with duplication. The FASTdRNA workflow is designed for the Snakemake framework and can be efficiently executed locally or in the cloud. Comparative experiments have demonstrated its superior performance compared to previous methods. This innovative workflow enhances the research capabilities of direct RNA-seq data analysis pipelines by optimizing existing processes and expanding the scope of analysis. Availability The workflow is freely available at https://github.com/Tomcxf/FASTdRNA under an MIT license. Detailed install and usage guidance can be found in the GitHub repository. Supplementary information Supplementary data are available at Bioinformatics Advances online.

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FASTdRNA: a workflow for the analysis of ONT direct RNA sequencing

Chen¹,

Liu²,

Lv³

et al. 2023

Bioinformatics Advances

View full text Add to dashboard Cite

show abstract

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RNA-seq Sample Preparation Kits Strongly Affect Transcriptome Profiles of a Gas-Fermenting Bacterium

Abstract: RNA-seq is a powerful technique for transcriptome profiling while involving elaborate sample processing before library sequencing. We show that RNA-seq library preparation kits can strongly affect the outcome of an RNA-seq experiment.

Cited by 1 publication

References 25 publications

FASTdRNA: a workflow for the analysis of ONT direct RNA sequencing

FASTdRNA: a workflow for the analysis of ONT direct RNA sequencing

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