ArticleBMC bioinformatics2018
ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- EPBAM: annotation-robust detection of alternative splicing events and a systematic benchmarking of current tools.Briefings in bioinformatics · 2026Article
- GFSeeker: a splicing-graph-based approach for accurate gene fusion detection from long-read RNA sequencing data.Briefings in bioinformatics · 2026Article
- Computational methods for alternative polyadenylation and splicing in post-transcriptional gene regulation.Experimental & molecular medicine · 2025Review
- Differential quantification of alternative splicing events on spliced pangenome graphs.PLoS computational biology · 2024Article
- RecGraph: recombination-aware alignment of sequences to variation graphs.Bioinformatics (Oxford, England) · 2024Article
- OutSplice: A Novel Tool for the Identification of Tumor-Specific Alternative Splicing Events.BioMedInformatics · 2023Article
- Counting pseudoalignments to novel splicing events.Bioinformatics (Oxford, England) · 2023Article
- Alternative splicing analysis benchmark with DICAST.NAR genomics and bioinformatics · 2023Article
- Article
- Therapeutic Vaccines Targeting Neoantigens to Induce T-Cell Immunity against Cancers.Pharmaceutics · 2022Review
- Computational graph pangenomics: a tutorial on data structures and their applications.Natural computing · 2022Article
- Alternative RNA splicing in stem cells and cancer stem cells: Importance of transcript-based expression analysis.World journal of stem cells · 2021Review
- McSplicer: a probabilistic model for estimating splice site usage from RNA-seq data.Bioinformatics (Oxford, England) · 2021Article
- Assessing conservation of alternative splicing with evolutionary splicing graphs.Genome research · 2021Article
- Shark: fishing relevant reads in an RNA-Seq sample.Bioinformatics (Oxford, England) · 2021Article
- Review
- Intron Retention as a Mode for RNA-Seq Data Analysis.Frontiers in genetics · 2020Review
- Yanagi: Fast and interpretable segment-based alternative splicing and gene expression analysis.BMC bioinformatics · 2019Article
- Alternative tumour-specific antigens.Nature reviews. Cancer · 2019Review
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundWhile the reconstruction of transcripts from a sample of RNA-Seq data is a computationally expensive and complicated task, the detection of splicing events from RNA-Seq data and a gene annotation is computationally feasible. This latter task, which is adequate for many transcriptome analyses, is usually achieved by aligning the reads to a reference genome, followed by comparing the alignments with a gene annotation, often implicitly represented by a graph: the splicing graph.
resultsWe present ASGAL (Alternative Splicing Graph ALigner): a tool for mapping RNA-Seq data to the splicing graph, with the specific goal of detecting novel splicing events, involving either annotated or unannotated splice sites. ASGAL takes as input the annotated transcripts of a gene and a RNA-Seq sample, and computes (1) the spliced alignments of each read in input, and (2) a list of novel events with respect to the gene annotation.
conclusionsAn experimental analysis shows that ASGAL allows to enrich the annotation with novel alternative splicing events even when genes in an experiment express at most one isoform. Compared with other tools which use the spliced alignment of reads against a reference genome for differential analysis, ASGAL better predicts events that use splice sites which are novel with respect to a splicing graph, showing a higher accuracy. To the best of our knowledge, ASGAL is the first tool that detects novel alternative splicing events by directly aligning reads to a splicing graph. AVAILABILITY: Source code, documentation, and data are available for download at http://asgal.algolab.eu .
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