JAGuaR: Junction Alignments to Genome for RNA-Seq Reads

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.

• Publication year

  2014

• Venue

  PLoS ONE

• Publication date

  2014-07-25

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1371/journal.pone.0102398PMID 25062255PMCID 4111418
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds

  2013cited by this paper
• STAR: ultrafast universal RNA-seq aligner

  2013cited by this paper
• PASTA: splice junction identification from RNA-Sequencing data

  2013cited by this paper
• TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

  2013influential reference
• Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift

  2012cited by this paper
• Modelling and simulating generic RNA-Seq experiments with the flux simulator

  2012cited by this paper
• A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

  2012cited by this paper
• TrueSight: a new algorithm for splice junction detection using RNA-seq

  2012cited by this paper
• TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

  2011cited by this paper
• SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data

  2011cited by this paper
• Ensembl 2012

  2011cited by this paper
• MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

  2010cited by this paper
• The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

  2010cited by this paper
• Fast and SNP-tolerant detection of complex variants and splicing in short reads

  2010influential reference
• Detection of splice junctions from paired-end RNA-seq data by SpliceMap

  2010cited by this paper
• The UCSC Genome Browser database: update 2011

  2010cited by this paper
• The UCSC Genome Browser database: update 2010

  2009cited by this paper
• The Sequence Alignment/Map format and SAMtools

  2009cited by this paper
• TopHat: discovering splice junctions with RNA-Seq

  2009cited by this paper
• Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

  2009cited by this paper
• The UCSC Genome Browser Database: update 2009

  2008cited by this paper
• Theoretical and practical advances in genome halving

  2004cited by this paper
• A Block-sorting Lossless Data Compression Algorithm

  1994cited by this paper

• Cell type-specific epigenomic variation and its association with genotype in the human breast

  2025cites this paper
• Whole genome and transcriptome integrated analyses guide clinical care of pediatric poor prognosis cancers

  2024influential citation
• Immune Activation Following Irbesartan Treatment in a Colorectal Cancer Patient: A Case Study

  2023cites this paper
• RUNX1 colludes with NOTCH1 to reprogram chromatin in T cell acute lymphoblastic leukemia

  2023cites this paper
• A high-throughput pipeline for DNA/RNA/small RNA purification from tissue samples for sequencing.

  2023cites this paper
• Benchmarking RNA Editing Detection Tools

  2023cites this paper
• The neoantigen landscape of the coding and noncoding cancer genome space.

  2022cites this paper
• Exceptional response to combination ipilimumab and nivolumab in metastatic uveal melanoma: Insights from genomic analysis

  2022cites this paper
• Dynamic spatiotemporal determinants modulate GPCR:G protein coupling selectivity and promiscuity

  2022cites this paper
• Whole-genome and transcriptome analysis of advanced adrenocortical cancer highlights multiple alterations affecting epigenome and DNA repair pathways

  2022cites this paper
• The impact of whole genome and transcriptome analysis (WGTA) on predictive biomarker discovery and diagnostic accuracy of advanced malignancies

  2022cites this paper
• Integrative multi‐omic analysis reveals neurodevelopmental gene dysregulation in CIC ‐knockout and IDH1 ‐mutant cells

  2021cites this paper
• Clinical response to nivolumab in an INI1-deficient pediatric chordoma correlates with immunogenic recognition of brachyury

  2021cites this paper
• Proteotranscriptomic classification and characterization of pancreatic neuroendocrine neoplasms.

  2021cites this paper
• A Scalable Strand-Specific Protocol Enabling Full-Length Total RNA Sequencing From Single Cells

  2021cites this paper
• A platform for oncogenomic reporting and interpretation

  2021cites this paper
• Genome and Transcriptome Biomarkers of Response to Immune Checkpoint Inhibitors in Advanced Solid Tumors

  2020cites this paper
• A comprehensive overview of computational tools for RNA-seq analysis

  2020cites this paper
• Uncovering Clinically Relevant Gene Fusions with Integrated Genomic and Transcriptomic Profiling of Metastatic Cancers

  2020cites this paper
• Glioma-derived IL-33 orchestrates an inflammatory brain tumor microenvironment that accelerates glioma progression

  2020cites this paper
• Pan-cancer analysis of advanced patient tumors reveals interactions between therapy and genomic landscapes

  2020cites this paper
• The Pathognomonic FOXL2 C134W Mutation Alters DNA-Binding Specificity

  2020cites this paper
• Endogenous Retrovirus Transcript Levels Are Associated with Immunogenic Signatures in Multiple Metastatic Cancer Types

  2020cites this paper
• Technology dictates algorithms: recent developments in read alignment

  2020cites this paper
• Epigenomic programming in early fetal brain development

  2020cites this paper
• Epigenetic and functional changes imposed by NUP98-HOXA9 in a genetically engineered model of chronic myeloid leukemia progression.

  2020cites this paper
• Evaluating genomic biomarkers associated with resistance or sensitivity to chemotherapy in patients with advanced breast and colorectal cancer

  2020cites this paper
• Identification and Analyses of Extra-Cranial and Cranial Rhabdoid Tumor Molecular Subgroups Reveal Tumors with Cytotoxic T Cell Infiltration

  2019cites this paper
• Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma.

  2019cites this paper
• Allele-Specific Transcript Abundance: A Pilot Study in Healthy Centenarians

  2019cites this paper
• Polycomb contraction differentially regulates terminal human hematopoietic differentiation programs

  2019cites this paper
• Comprehensive genomic profiling of glioblastoma tumors, BTICs, and xenografts reveals stability and adaptation to growth environments

  2019cites this paper
• Altered Gene Expression along the Glycolysis–Cholesterol Synthesis Axis Is Associated with Outcome in Pancreatic Cancer

  2019cites this paper
• SLUG Directs the Precursor State of Human Brain Tumor Stem Cells

  2019cites this paper
• Evaluation of protocols for rRNA depletion-based RNA sequencing of nanogram inputs of mammalian total RNA

  2019cites this paper
• Fluorouracil sensitivity in a head and neck squamous cell carcinoma with a somatic DPYD structural variant

  2019cites this paper
• Personalized oncogenomic analysis of metastatic adenoid cystic carcinoma: using whole-genome sequencing to inform clinical decision-making

  2018cites this paper
• RUNX1 promotes cell growth in human T-cell acute lymphoblastic leukemia by transcriptional regulation of key target genes.

  2018cites this paper
• A case study of apparent immune activation following treatment of a colorectal cancer patient with an angiotensin receptor blocker

  2018influential citation
• Mechanisms of acute leukemia disease initiation and maintenance through manipulation of IGF1R and RUNX family members.

  2017cites this paper
• Assessment of a potential therapeutic target in the Hedgehog pathway for the eradication of primitive chronic myeloid leukemia cells

  2017cites this paper
• A Survey of Bioinformatics-Based Tools in RNA-Sequencing (RNA-Seq) Data Analysis

  2017cites this paper
• Homologous Recombination Deficiency and Platinum-Based Therapy Outcomes in Advanced Breast Cancer

  2017cites this paper
• Detection and genomic characterization of a mammary-like adenocarcinoma

  2017influential citation
• Automated high throughput nucleic acid purification from formalin-fixed paraffin-embedded tissue samples for next generation sequence analysis

  2017cites this paper
• Bioinformatic approaches for identifying single nucleotide variants and profiling alternative expression in cancer transcriptomes

  2017cites this paper
• Personalized oncogenomics in the management of gastrointestinal carcinomas-early experiences from a pilot study.

  2016cites this paper
• Novel computational techniques for mapping and classifying Next-Generation Sequencing data. (Nouvelles techniques informatiques pour la localisation et la classification de données de séquençage haut débit)

  2016cites this paper
• Molecular etiology of an indolent lymphoproliferative disorder determined by whole-genome sequencing

  2016cites this paper
• Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress

  2016cites this paper
• Divergent clonal selection dominates medulloblastoma at recurrence

  2016cites this paper
• Integrative analysis of 111 reference human epigenomes

  2015cites this paper
• Barcoding reveals complex clonal dynamics of de novo transformed human mammary cells

  2015cites this paper
• Analysis of genome activation in early bovine embryos by bioinformatic evaluation of RNA-Seq data

  2015cites this paper
• Engineering Algorithms for Personal Genome Pipelines

  2015cites this paper
• Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs

  2015cites this paper
• Epigenetic and transcriptional determinants of the human breast

  2015cites this paper