ArticleNucleic acids research2010
MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 613 papers.
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Who cites it
613 citing papers in PubMed.
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- The MEK inhibitor trametinib incurs mitochondrial injury and induces innate immune responses in the mouse heart.Science advances · 2026Article
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- Spliceread: improving canonical and non-canonical splice site prediction with residual blocks and synthetic data augmentation.BMC bioinformatics · 2026Article
- Detection of Candidate Circular RNAs to Monitor Anti-Hormonal Response in the Mammary Gland.bioRxiv : the preprint server for biology · 2026Article
- SpliceRead: Improving Canonical and Non-Canonical Splice Site Prediction with Residual Blocks and Synthetic Data Augmentation.bioRxiv : the preprint server for biology · 2026Article
- Opportunities for RNA sequencing in physiology: from big data to understanding homeostasis and heterogeneity.Function (Oxford, England) · 2026Review
- Integrative Chimeric RNA Prediction with FASfuse.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A unified model for Duchenne muscular dystrophy gene involvement in cancer: context-dependent tumour suppression and oncogenicity.FEBS open bio · 2026Article
- Circular RNAs in Cardiovascular Physiopathology: From Molecular Mechanisms to Therapeutic Opportunities.International journal of molecular sciences · 2025Review
- Tracing the evolution of sequencing into the era of genomic medicine.Nature reviews. Genetics · 2025Review
- MitoDelta: identifying mitochondrial DNA deletions at cell-type resolution from single-cell RNA sequencing data.BMC genomics · 2025Article
- EWS::WT1 Isoform-Dependent Regulation of Neogenes in Desmoplastic Small Round Cell Tumors.bioRxiv : the preprint server for biology · 2025Article
- The MEK inhibitor trametinib incurs mitochondrial injury and induces innate immune responses in the mouse heart.bioRxiv : the preprint server for biology · 2025Article
- Proteogenomic characterization of invasive breast tumors in young women.NPJ breast cancer · 2025Article
- Distinct Mitochondrial DNA Deletion Profiles in Pediatric B- and T-ALL During Diagnosis, Remission, and Relapse.International journal of molecular sciences · 2025Article
- Prevalence and biological impact of clinically relevant gene fusions in head and neck cancers.NPJ precision oncology · 2025Article
- Comparative transcriptomics of salivary basal cell adenoma and adenocarcinoma sustain linear neoplastic evolution and intertumor heterogeneity: classification and biological implications.The Journal of pathology · 2025Article
553 more citing papers are in PubMed but not listed here.
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Authors and funding
14 authors.
Funding
Abstract
The accurate mapping of reads that span splice junctions is a critical component of all analytic techniques that work with RNA-seq data. We introduce a second generation splice detection algorithm, MapSplice, whose focus is high sensitivity and specificity in the detection of splices as well as CPU and memory efficiency. MapSplice can be applied to both short (<75 bp) and long reads (≥ 75 bp). MapSplice is not dependent on splice site features or intron length, consequently it can detect novel canonical as well as non-canonical splices. MapSplice leverages the quality and diversity of read alignments of a given splice to increase accuracy. We demonstrate that MapSplice achieves higher sensitivity and specificity than TopHat and SpliceMap on a set of simulated RNA-seq data. Experimental studies also support the accuracy of the algorithm. Splice junctions derived from eight breast cancer RNA-seq datasets recapitulated the extensiveness of alternative splicing on a global level as well as the differences between molecular subtypes of breast cancer. These combined results indicate that MapSplice is a highly accurate algorithm for the alignment of RNA-seq reads to splice junctions. Software download URL: http://www.netlab.uky.edu/p/bioinfo/MapSplice.
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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.