ArticleBMC bioinformatics2021
Computational comparison of common event-based differential splicing tools: practical considerations for laboratory researchers.
Article in BMC bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Benchmarking RNA-seq with the Quartet and MAQC reference materials to establish best practices for accurate alternative splicing analysis.Nature communications · 2026Article
- Determining off-target effects of splice-switching antisense oligonucleotides using short read RNAseq in neuronally differentiated human induced pluripotent stem cells.Human molecular genetics · 2025Article
- Article
- Nanopore-Based Sequencing of the Full-Length Transcriptome of Male and Female Cleavage-Stage Embryos of the Chinese Mitten Crab (International journal of molecular sciences · 2024Article
- Loss-of-function mutation in PRMT9 causes abnormal synapse development by dysregulation of RNA alternative splicing.Nature communications · 2024Article
- Widespread alternative splicing dysregulation occurs presymptomatically in CAG expansion spinocerebellar ataxias.Brain : a journal of neurology · 2024Article
- KDM3A and KDM3B Maintain Naïve Pluripotency Through the Regulation of Alternative Splicing.bioRxiv : the preprint server for biology · 2024Article
- Identification of Splice Variants and Isoforms in Transcriptomics and Proteomics.Annual review of biomedical data science · 2023Review
- Methotrexate Provokes Disparate Folate Metabolism Gene Expression and Alternative Splicing in Ex Vivo Monocytes and GM-CSF- and M-CSF-Polarized Macrophages.International journal of molecular sciences · 2023Article
- Transcriptomic Complexity of Culm Growth and Development in Different Types of Moso Bamboo.International journal of molecular sciences · 2023Review
- Unveiling the Role of Dynamic Alternative Splicing Modulation After Infestation with Sea Lice (Caligus rogercresseyi) in Atlantic Salmon.Marine biotechnology (New York, N.Y.) · 2023Article
- Transcriptome analysis provides critical answers to the "variants of uncertain significance" conundrum.Human mutation · 2022Review
- Epigenetic Alterations in Cryopreserved Human Spermatozoa: Suspected Potential Functional Defects.Cells · 2022Article
- Reversal of splicing infidelity is a pre-activation step in B cell differentiation.Frontiers in immunology · 2022Article
- Probing Isoform Switching Events in Various Cancer Types: Lessons From Pan-Cancer Studies.Frontiers in molecular biosciences · 2021Review
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundComputational tools analyzing RNA-sequencing data have boosted alternative splicing research by identifying and assessing differentially spliced genes. However, common alternative splicing analysis tools differ substantially in their statistical analyses and general performance. This report compares the computational performance (CPU utilization and RAM usage) of three event-level splicing tools; rMATS, MISO, and SUPPA2. Additionally, concordance between tool outputs was investigated.
resultsLog-linear relations were found between job times and dataset size in all splicing tools and all virtual machine (VM) configurations. MISO had the highest job times for all analyses, irrespective of VM size, while MISO analyses also exceeded maximum CPU utilization on all VM sizes. rMATS and SUPPA2 load averages were relatively low in both size and replicate comparisons, not nearing maximum CPU utilization in the VM simulating the lowest computational power (D2 VM). RAM usage in rMATS and SUPPA2 did not exceed 20% of maximum RAM in both size and replicate comparisons while MISO reached maximum RAM usage in D2 VM analyses for input size. Correlation coefficients of differential splicing analyses showed high correlation (β > 80%) between different tool outputs with the exception of comparisons of retained intron (RI) events between rMATS/MISO and rMATS/SUPPA2 (β < 60%).
conclusionsPrior to RNA-seq analyses, users should consider job time, amount of replicates and splice event type of interest to determine the optimal alternative splicing tool. In general, rMATS is superior to both MISO and SUPPA2 in computational performance. Analysis outputs show high concordance between tools, with the exception of RI events.
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