ArticlePloS one2016
Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis Tools.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Practical RNA-Seq with Spike-Ins: A Bench-to-Bioinformatics Guide.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Integrative and accurate annotations enhance current nonsense-mediated mRNA decay rules.Nucleic acids research · 2025Article
- Alternative splicing analysis benchmark with DICAST.NAR genomics and bioinformatics · 2023Article
- Protocol for transcriptome assembly by the TransBorrow algorithm.Biology methods & protocols · 2023Review
- Exploring differential exon usage via short- and long-read RNA sequencing strategies.Open biology · 2022Article
- Gene expression analysis method integration and co-expression module detection applied to rare glucide metabolism disorders using ExpHunterSuite.Scientific reports · 2021Article
- RNA sequencing: the teenage years.Nature reviews. Genetics · 2019Review
- A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs.Life science alliance · 2019Article
- Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts.Computational and structural biotechnology journal · 2019Review
- Reference standards for next-generation sequencing.Nature reviews. Genetics · 2017Review
- RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samples.BMC genomics · 2017Article
- Cutaneous transcriptome analysis in NIH hairless mice.PloS one · 2017Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
One of the key applications of next-generation sequencing (NGS) technologies is RNA-Seq for transcriptome genome-wide analysis. Although multiple studies have evaluated and benchmarked RNA-Seq tools dedicated to gene level analysis, few studies have assessed their effectiveness on the transcript-isoform level. Alternative splicing is a naturally occurring phenomenon in eukaryotes, significantly increasing the biodiversity of proteins that can be encoded by the genome. The aim of this study was to assess and compare the ability of the bioinformatics approaches and tools to assemble, quantify and detect differentially expressed transcripts using RNA-Seq data, in a controlled experiment. To this end, in vitro synthesized mouse spike-in control transcripts were added to the total RNA of differentiating mouse embryonic bodies, and their expression patterns were measured. This novel approach was used to assess the accuracy of the tools, as established by comparing the observed results versus the results expected of the mouse controlled spiked-in transcripts. We found that detection of differential expression at the gene level is adequate, yet on the transcript-isoform level, all tools tested lacked accuracy and precision.
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