JAGuaR

Junction Alignments to Genome for RNA-seq Reads

Project Description

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.

JAGuaR paper/reference in PLOS ONE

Documentation

Examples and associated files