ArticleScientific reports2018
Complementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed.
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- Sexual Antagonism and Sex Determination in Three Syngnathid Species Alongside a Male Pregnancy Gradient.Genome biology and evolution · 2025Article
- De novo transcriptome assembly of the Perna viridis: A novel invertebrate model for ecotoxicological studies.Scientific data · 2025Article
- Altered drug metabolism and increased susceptibility to fatty liver disease in a mouse model of myotonic dystrophy.Nature communications · 2024Article
- Accelerated DNA replication fork speed due to loss of R-loops in myelodysplastic syndromes with SF3B1 mutation.Nature communications · 2024Article
- Gene-to-gene coordinated regulation of transcription and alternative splicing by 3D chromatin remodeling upon NF-κB activation.Nucleic acids research · 2024Article
- SplicingLore: a web resource for studying the regulation of cassette exons by human splicing factors.Database : the journal of biological databases and curation · 2023Article
- Mutations in the non-coding RNU4ATAC gene affect the homeostasis and function of the Integrator complex.Nucleic acids research · 2023Article
- Altered splicing of ATG16-L1 mediates acquired resistance to tyrosine kinase inhibitors of EGFR by blocking autophagy in non-small cell lung cancer.Molecular oncology · 2022Article
- Myotonic dystrophy RNA toxicity alters morphology, adhesion and migration of mouse and human astrocytes.Nature communications · 2022Article
- The endogenous HBZ interactome in ATL leukemic cells reveals an unprecedented complexity of host interacting partners involved in RNA splicing.Frontiers in immunology · 2022Article
- Modulation of alternative splicing during early infection of human primary B lymphocytes with Epstein-Barr virus (EBV): a novel function for the viral EBNA-LP protein.Nucleic acids research · 2021Article
- Shark: fishing relevant reads in an RNA-Seq sample.Bioinformatics (Oxford, England) · 2021Article
- Integrative Cell Type-Specific Multi-Omics Approaches Reveal Impaired Programs of Glial Cell Differentiation in Mouse Culture Models of DM1.Frontiers in cellular neuroscience · 2021Article
- Alternative splicing: Human disease and quantitative analysis from high-throughput sequencing.Computational and structural biotechnology journal · 2021Review
- Influenza virus infection induces widespread alterations of host cell splicing.NAR genomics and bioinformatics · 2020Article
- Comprehensive temporal reprogramming ensures dynamicity of transcriptomic profile for adaptive response in Taxus contorta.Molecular genetics and genomics : MGG · 2020Article
- Intragenic recruitment of NF-κB drives splicing modifications upon activation by the oncogene Tax of HTLV-1.Nature communications · 2020Article
- ZRANB2 and SYF2-mediated splicing programs converging on ECT2 are involved in breast cancer cell resistance to doxorubicin.Nucleic acids research · 2020Article
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14 authors.
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Abstract
Genome-wide analyses estimate that more than 90% of multi exonic human genes produce at least two transcripts through alternative splicing (AS). Various bioinformatics methods are available to analyze AS from RNAseq data. Most methods start by mapping the reads to an annotated reference genome, but some start by a de novo assembly of the reads. In this paper, we present a systematic comparison of a mapping-first approach (FARLINE) and an assembly-first approach (KISSPLICE). We applied these methods to two independent RNAseq datasets and found that the predictions of the two pipelines overlapped (70% of exon skipping events were common), but with noticeable differences. The assembly-first approach allowed to find more novel variants, including novel unannotated exons and splice sites. It also predicted AS in recently duplicated genes. The mapping-first approach allowed to find more lowly expressed splicing variants, and splice variants overlapping repeats. This work demonstrates that annotating AS with a single approach leads to missing out a large number of candidates, many of which are differentially regulated across conditions and can be validated experimentally. We therefore advocate for the combined use of both mapping-first and assembly-first approaches for the annotation and differential analysis of AS from RNAseq datasets.
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