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PLoS One. 2014 Jul 25;9(7):e102398. doi: 10.1371/journal.pone.0102398. eCollection 2014.

JAGuaR: junction alignments to genome for RNA-seq reads.

Author information

1
Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.

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.

PMID:
25062255
PMCID:
PMC4111418
DOI:
10.1371/journal.pone.0102398
[Indexed for MEDLINE]
Free PMC Article

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