JAGuaR: junction alignments to genome for RNA-seq reads

• Published in: PloS one Vol. 9; no. 7; p. e102398
• Main Authors: Butterfield, Yaron S, Kreitzman, Maayan, Thiessen, Nina, Corbett, Richard D, Li, Yisu, Pang, Johnson, Ma, Yussanne P, Jones, Steven J M, Birol, İnanç
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 25.07.2014; Public Library of Science (PLoS)
• Subjects: Acids; Algorithms; Alignment; Analysis; Animals; Base Sequence; Bioinformatics; Biology and Life Sciences; Computer and Information Sciences; Data compression; Drosophila melanogaster; Exons; Gene expression; Gene Expression Profiling - methods; Genomes; Genomics; High-Throughput Nucleotide Sequencing; Humans; Insects; Physical Sciences; Ribonucleic acid; RNA; RNA - genetics; RNA Splicing - genetics; Sequence Alignment - methods; Sequence Analysis, RNA - methods; Software; Transcription; Canada
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0102398

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.