ArticlePloS one2014
JAGuaR: junction alignments to genome for RNA-seq reads.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
31 citing papers in PubMed.
- Whole genome and transcriptome integrated analyses guide clinical care of pediatric poor prognosis cancers.Nature communications · 2024Article
- Benchmarking RNA Editing Detection Tools.Biotech (Basel (Switzerland)) · 2023Review
- RUNX1 colludes with NOTCH1 to reprogram chromatin in T cell acute lymphoblastic leukemia.iScience · 2023Article
- Immune Activation following Irbesartan Treatment in a Colorectal Cancer Patient: A Case Study.International journal of molecular sciences · 2023Article
- Dynamic spatiotemporal determinants modulate GPCR:G protein coupling selectivity and promiscuity.Nature communications · 2022Article
- The impact of whole genome and transcriptome analysis (WGTA) on predictive biomarker discovery and diagnostic accuracy of advanced malignancies.The journal of pathology. Clinical research · 2022Article
- Polycomb contraction differentially regulates terminal human hematopoietic differentiation programs.BMC biology · 2022Article
- Whole-genome and transcriptome analysis of advanced adrenocortical cancer highlights multiple alterations affecting epigenome and DNA repair pathways.Cold Spring Harbor molecular case studies · 2022Article
- Integrative multi-omic analysis reveals neurodevelopmental gene dysregulation in CIC-knockout and IDH1-mutant cells.The Journal of pathology · 2022Article
- A platform for oncogenomic reporting and interpretation.Nature communications · 2022Article
- Clinical response to nivolumab in an INI1-deficient pediatric chordoma correlates with immunogenic recognition of brachyury.NPJ precision oncology · 2021Article
- Technology dictates algorithms: recent developments in read alignment.Genome biology · 2021Review
- A Scalable Strand-Specific Protocol Enabling Full-Length Total RNA Sequencing From Single Cells.Frontiers in genetics · 2021Article
- Glioma-derived IL-33 orchestrates an inflammatory brain tumor microenvironment that accelerates glioma progression.Nature communications · 2020Article
- Allele-Specific Transcript Abundance: A Pilot Study in Healthy Centenarians.The journals of gerontology. Series A, Biological sciences and medical sciences · 2020Article
- Pan-cancer analysis of advanced patient tumors reveals interactions between therapy and genomic landscapes.Nature cancer · 2020Article
- Fluorouracil sensitivity in a head and neck squamous cell carcinoma with a somaticCold Spring Harbor molecular case studies · 2020Article
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- Comprehensive genomic profiling of glioblastoma tumors, BTICs, and xenografts reveals stability and adaptation to growth environments.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
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Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
JAGuaR is an alignment protocol for RNA-seq reads that uses an extended reference to increase alignment sensitivity. It uses BWA to align reads to the genome and reference transcript models (including annotated exon-exon junctions) specifically allowing for the possibility of a single read spanning multiple exons. Reads aligned to the transcript models are then re-mapped on to genomic coordinates, transforming alignments that span multiple exons into large-gapped alignments on the genome. While JAGuaR does not detect novel junctions, we demonstrate how JAGuaR generates fast and accurate transcriptome alignments, which allows for both sensitive and specific SNV calling.
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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.