ArticleNucleic acids research2014
FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- The Genome-Wide Characterization of Alternative Splicing and RNA Editing in the Development ofJournal of fungi (Basel, Switzerland) · 2023Article
- 2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing.Genome biology · 2021Article
- Discerning novel splice junctions derived from RNA-seq alignment: a deep learning approach.BMC genomics · 2018Article
- Efficient and accurate detection of splice junctions from RNA-seq with Portcullis.GigaScience · 2018Article
- Genome-wide profiling of differentially spliced mRNAs in human fetal cortical tissue exposed to alcohol.Alcohol (Fayetteville, N.Y.) · 2017Article
- Comparison of Alternative Splicing Junction Detection Tools Using RNA-Seq Data.Current genomics · 2017Review
- Gene expression atlas of pigeonpea and its application to gain insights into genes associated with pollen fertility implicated in seed formation.Journal of experimental botany · 2017Article
- The exon quantification pipeline (EQP): a comprehensive approach to the quantification of gene, exon and junction expression from RNA-seq data.Nucleic acids research · 2016Article
- A Developmental Transcriptome Map for AllotetraploidFrontiers in plant science · 2016Article
- Two-pass alignment improves novel splice junction quantification.Bioinformatics (Oxford, England) · 2016Article
- Computational Identification of Novel Genes: Current and Future Perspectives.Bioinformatics and biology insights · 2016Review
- A survey of computational methods in transcriptome-wide alternative splicing analysis.Biomolecular concepts · 2015Review
- RNA-Seq: Improving Our Understanding of Retinal Biology and Disease.Cold Spring Harbor perspectives in medicine · 2015Review
- RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application.BMC genomics · 2015Article
- An improved understanding of cancer genomics through massively parallel sequencing.Translational cancer research · 2014Article
- Transcriptome complexity in cardiac development and diseases--an expanding universe between genome and phenome.Circulation journal : official journal of the Japanese Circulation Society · 2014Review
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Alternative splicing is the main mechanism governing protein diversity. The recent developments in RNA-Seq technology have enabled the study of the global impact and regulation of this biological process. However, the lack of standardized protocols constitutes a major bottleneck in the analysis of alternative splicing. This is particularly important for the identification of exon-exon junctions, which is a critical step in any analysis workflow. Here we performed a systematic benchmarking of alignment tools to dissect the impact of design and method on the mapping, detection and quantification of splice junctions from multi-exon reads. Accordingly, we devised a novel pipeline based on TopHat2 combined with a splice junction detection algorithm, which we have named FineSplice. FineSplice allows effective elimination of spurious junction hits arising from artefactual alignments, achieving up to 99% precision in both real and simulated data sets and yielding superior F1 scores under most tested conditions. The proposed strategy conjugates an efficient mapping solution with a semi-supervised anomaly detection scheme to filter out false positives and allows reliable estimation of expressed junctions from the alignment output. Ultimately this provides more accurate information to identify meaningful splicing patterns. FineSplice is freely available at https://sourceforge.net/p/finesplice/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.