A benchmarking of workflows for detecting differential splicing and differential expression at isoform level in human RNA-seq studies

  title={A benchmarking of workflows for detecting differential splicing and differential expression at isoform level in human RNA-seq studies},
  author={Gabriela Alejandra Merino and Ana Conesa and Elmer Andr{\'e}s Fern{\'a}ndez},
Over the last few years, RNA-seq has been used to study alterations in alternative splicing related to several diseases. [] Key Method We evaluated the workflows performance over different experimental scenarios where changes in absolute and relative isoform expression occurred simultaneously. In addition, the effect of the number of isoforms per gene, and the magnitude of the expression change over pipeline performances were also evaluated. Our results suggest that workflow performance is influenced by the…

Figures and Tables from this paper

Alternative splicing analysis benchmark with DICAST

DICAST offers a modular and extensible framework for the analysis of alternative splicing integrating 11 splice-aware mapping and eight event detection tools and proposes the first reporting standard to unify existing formats and to guide future tool development.

Empirical assessment of the impact of sample number and read depth on RNA-Seq analysis workflow performance

This analysis focuses on 30 high-performing workflows, systematically varying the read depth and number of biological replicates of patient monocyte samples provided as input, finding that, in general, read depth has little effect on workflow performance when held above two million reads per sample, with reduced workflow performance below this threshold.

LncAS2Cancer: a comprehensive database for alternative splicing of lncRNAs across human cancers

A comprehensive database focusing on cancer-related alternative splicing of lncRNAs, which can not only confirm the known cancer-associated lncRNA isoforms but also indicate novel ones, is developed, and a reliable score to prioritize splicing events for further elucidation is proposed.

Factorial study of the RNA-seq computational workflow identifies biases as technical gene signatures

This work highlights the yet inadequately characterized central importance of genome annotations in quantification results, and offers an explanation for the observed biases by identifying the common features used differently by the software and references, therefore providing leads for the betterment of RNA-seq methodology.

Comparative evaluation of full-length isoform quantification from RNA-Seq

The tested methods show sufficient divergence from the truth to suggest that full-length isoform quantification and isoform level DE should still be employed selectively and the structural parameters with the greatest impact on quantification accuracy to be length and sequence compression complexity and not so much the number of isoforms.

Impact of RNA-seq data analysis algorithms on gene expression estimation and downstream prediction

It was found that RNA-seq pipeline components jointly and significantly impacted the accuracy of gene expression estimation, and its impact was extended to the downstream prediction of these cancer outcomes.

Maternal methionine supplementation during gestation alters alternative splicing and DNA methylation in bovine skeletal muscle

Evidence is provided that a prenatal diet rich in methyl donors can significantly alter the offspring transcriptome, including changes in isoform expression and exon usage, and some of these changes are mediated by changes in DNA methylation.

Demystifying emerging bulk RNA-Seq applications: the application and utility of bioinformatic methodology.

The focus of this review is to comprehend the emerging Bulk RNA-Seq-based analyses, emphasizing less familiar and underused applications and highlighting the power of bulk RNA- Seq in providing biological insights.

Analysis of long non-coding RNA and mRNA expression in bovine macrophages brings up novel aspects of Mycobacterium avium subspecies paratuberculosis infections

This study investigated the alteration in genomic expression profiles of mRNA and lncRNA in bovine macrophages in response to Paratuberculosis infection using RNA-Seq and identified 397 potentially novel lncRNAs in macrophage candidates, of which 38 were differentially regulated by the infection.



SplicingCompass: differential splicing detection using RNA-Seq data

A new method and software to predict genes that are differentially spliced between two different conditions using RNA-seq data using geometric angles between the high dimensional vectors of exon read counts is presented and could successfully exploit splicing information to cluster tissues and patients.

A survey of computational methods in transcriptome-wide alternative splicing analysis

The currently available computational approaches for the analysis of RNA-sequencing data with a focus on exon-skipping events of alternative splicing are reviewed and the novelties as well as challenges faced to perform differential splicing analyses are discussed.

Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems

This study compares the eight popular public available software packages for differential splicing analysis using both simulated and real Arabidopsis thaliana RNA-seq data to benchmark existing computational differentialsplicing detection methods so that biologists can choose the most suitable tools to accomplish their goals.

Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data

It is found that many tools have good accuracy and yield better estimates of gene-level expression compared to commonly used count-based approaches, but they vary widely in memory and runtime requirements.

Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage

It is shown that an incomplete annotation catalog can have a detrimental effect on the ability to detect differential transcript usage in transcriptomes with few isoforms per gene and that isoform-level prefiltering can considerably improve false discovery rate control.

Detecting differential usage of exons from RNA-seq data.

DEXSeq is presented, a statistical method to test for differential exon usage in RNA-seq data that uses generalized linear models and offers reliable control of false discoveries by taking biological variation into account.

A survey of software for genome-wide discovery of differential splicing in RNA-Seq data

Three approaches to differential splicing analysis are described, along with their associated software implementations, their strengths, limitations, and caveats, and suggestions for future work include more extensive experimental validation to assess accuracy of the software predictions and consensus formats for outputs.

Methods to study splicing from high-throughput RNA sequencing data.

An overview of the methods available to study splicing from short RNA-Seq data is provided, which could serve as an entry point for users who need to decide on a suitable tool for a specific analysis, and a classification of the tools according to the operations they do is proposed to facilitate the comparison and choice of methods.

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.

The results suggest that Cufflinks can illuminate the substantial regulatory flexibility and complexity in even this well-studied model of muscle development and that it can improve transcriptome-based genome annotation.

Alternative Isoform Regulation in Human Tissue Transcriptomes

An in-depth analysis of 15 diverse human tissue and cell line transcriptomes on the basis of deep sequencing of complementary DNA fragments yielding a digital inventory of gene and mRNA isoform expression suggested common involvement of specific factors in tissue-level regulation of both splicing and polyadenylation.