JAGuaR 2.1 – Junction Alignment to Genome for Repositioning RNA-seq Reads

JAGuaR 2.1

:: 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.

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::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

  JAGuaR

:: MORE INFORMATION

Citation

Butterfield YS, Kreitzman M, Thiessen N, Corbett RD, Li Y, Pang J, Ma YP, Jones SJ, Birol İ.
JAGuaR: junction alignments to genome for RNA-seq reads.
PLoS One. 2014 Jul 25;9(7):e102398. doi: 10.1371/journal.pone.0102398. PMID: 25062255; PMCID: PMC4111418.