title: JAGuaR: junction alignments to genome for RNA-seq reads.
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.
authors: Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.
authors: Yaron S
authors: YS
authors: Butterfield
authors: Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.
authors: Maayan
authors: M
authors: Kreitzman
authors: Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.
authors: Nina
authors: N
authors: Thiessen
authors: Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.
authors: Richard D
authors: RD
authors: Corbett
authors: Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.
authors: Yisu
authors: Y
authors: Li
authors: Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.
authors: Johnson
authors: J
authors: Pang
authors: Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.
authors: Yussanne P
authors: YP
authors: Ma
authors: Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.
authors: Steven J M
authors: SJ
authors: Jones
authors: Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.
authors: İnanç
authors: İ
authors: Birol
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D005091:Exons; D020869:Gene Expression Profiling / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D012313:RNA / Q000235:genetics*; D012326:RNA Splicing / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012313:RNA