Alternative splicing analysis benchmark with DICAST.
Journal
NAR genomics and bioinformatics
ISSN: 2631-9268
Titre abrégé: NAR Genom Bioinform
Pays: England
ID NLM: 101756213
Informations de publication
Date de publication:
Jun 2023
Jun 2023
Historique:
received:
04
07
2022
revised:
13
04
2023
accepted:
05
05
2023
medline:
1
6
2023
pubmed:
1
6
2023
entrez:
1
6
2023
Statut:
epublish
Résumé
Alternative splicing is a major contributor to transcriptome and proteome diversity in health and disease. A plethora of tools have been developed for studying alternative splicing in RNA-seq data. Previous benchmarks focused on isoform quantification and mapping. They neglected event detection tools, which arguably provide the most detailed insights into the alternative splicing process. DICAST offers a modular and extensible framework for analysing alternative splicing integrating eleven splice-aware mapping and eight event detection tools. We benchmark all tools extensively on simulated as well as whole blood RNA-seq data. STAR and HISAT2 demonstrated the best balance between performance and run time. The performance of event detection tools varies widely with no tool outperforming all others. DICAST allows researchers to employ a consensus approach to consider the most successful tools jointly for robust event detection. Furthermore, we propose the first reporting standard to unify existing formats and to guide future tool development.
Identifiants
pubmed: 37260511
doi: 10.1093/nargab/lqad044
pii: lqad044
pmc: PMC10227362
doi:
Types de publication
Journal Article
Langues
eng
Pagination
lqad044Informations de copyright
© The Author(s) 2023. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.
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