Junction Alignment to Genome for Repositioning RNA-seq Reads
JAGuaR is an alignment protocol for paired end RNA-seq reads based on an extended reference. It uses BWA to align reads to the genome and reference transcript models (including annotated exon-exon junctions) specifically allowing the possibility for a single read to span multiple exons. Reads aligned to the special reference repository are then “repositioned” on to genomic coordinates, transforming reads spanning multiple exons into large-gapped alignments. We demonstrate that the strategy employed by JAGuaR generates accurate transcriptome alignments, measured by the concordance of inferred SNVs with dbSNP
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Released Sep 12, 2013
Latest stable release.
More about this release…
- Get JAGuaR for all platforms
- JAGuaR 2.1
- If you are using Plone 3.2 or higher, you probably want to install this product with buildout. See our tutorial on installing add-on products with buildout for more information.