ArticleNucleic acids research2013
TrueSight: a new algorithm for splice junction detection using RNA-seq.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Detection of alternative splicing: deep sequencing or deep learning?Briefings in bioinformatics · 2026Article
- Extent and complexity of RNA processing in honey bee queen and worker caste development.iScience · 2022Article
- Modern Approaches for Transcriptome Analyses in Plants.Advances in experimental medicine and biology · 2021Article
- Comparative Analysis of Brain and Fat Body Gene Splicing Patterns in the Honey Bee,G3 (Bethesda, Md.) · 2019Article
- RNAiSeq: How to See the Big Picture.Frontiers in microbiology · 2019Review
- 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
- Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis).GigaScience · 2018Article
- Comparison of Alternative Splicing Junction Detection Tools Using RNA-Seq Data.Current genomics · 2017Review
- Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data.BMC genomics · 2016Article
- RBM4a-regulated splicing cascade modulates the differentiation and metabolic activities of brown adipocytes.Scientific reports · 2016Article
- The evolutionary landscape of intergenic trans-splicing events in insects.Nature communications · 2015Article
- RNA-Seq: Improving Our Understanding of Retinal Biology and Disease.Cold Spring Harbor perspectives in medicine · 2015Review
- SpliceJumper: a classification-based approach for calling splicing junctions from RNA-seq data.BMC bioinformatics · 2015Article
- RNA-seq Data: Challenges in and Recommendations for Experimental Design and Analysis.Current protocols in human genetics · 2014Article
- Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm.Nucleic acids research · 2014Article
- FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions.Nucleic acids research · 2014Article
- UnSplicer: mapping spliced RNA-Seq reads in compact genomes and filtering noisy splicing.Nucleic acids research · 2014Article
- JAGuaR: junction alignments to genome for RNA-seq reads.PloS one · 2014Article
- Novel bioinformatics method for identification of genome-wide non-canonical spliced regions using RNA-Seq data.PloS one · 2014Article
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6 authors.
Funding
Abstract
RNA-seq has proven to be a powerful technique for transcriptome profiling based on next-generation sequencing (NGS) technologies. However, due to the short length of NGS reads, it is challenging to accurately map RNA-seq reads to splice junctions (SJs), which is a critically important step in the analysis of alternative splicing (AS) and isoform construction. In this article, we describe a new method, called TrueSight, which for the first time combines RNA-seq read mapping quality and coding potential of genomic sequences into a unified model. The model is further utilized in a machine-learning approach to precisely identify SJs. Both simulations and real data evaluations showed that TrueSight achieved higher sensitivity and specificity than other methods. We applied TrueSight to new high coverage honey bee RNA-seq data to discover novel splice forms. We found that 60.3% of honey bee multi-exon genes are alternatively spliced. By utilizing gene models improved by TrueSight, we characterized AS types in honey bee transcriptome. We believe that TrueSight will be highly useful to comprehensively study the biology of alternative splicing.
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