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

JAGuaR: junction alignments to genome for RNA-seq reads

Yaron S Butterfield  1 , Maayan Kreitzman  1 , Nina Thiessen  1 , Richard D Corbett  1 , Yisu Li  1 , Johnson Pang  1 , Yussanne P Ma  1 , Steven J M Jones  1 , İnanç Birol  1
Affiliations

JAGuaR: junction alignments to genome for RNA-seq reads

Yaron S Butterfield et al. PLoS One. .

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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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. SNV concordance between tools for one read set (Sample 2).
a) Number of variants in dbSNP (v137) plotted against number of variants called at various levels of depth. Depth begins on far right at 6 bp and each point represents increasing depth of 1 bp coverage. b) Overlap of known SNVs called c) Overlap of known non-synonymous SNVs called d) Overlap of SNVs called in COSMIC. All SNP calls were assessed at depth of 6. *BWA-MEM.
See this image and copyright information in PMC

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References

    1. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25(9): 1105–11. - PMC - PubMed
    1. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, et al. (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology 14: R36. - PMC - PubMed
    1. Burrows M, Wheeler DJ (1994) A block-sorting lossless data compression algorithm.Technical report 124. Palo Alto, CA: Digital Equipment Corporation.
    1. Wu TD, Nacu S (2010) Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26 (7): 873–881. - PMC - PubMed
    1. Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, et al.. (2010) MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res. 38(18). - PMC - PubMed

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