Illumina paired-end RNA sequencing data was aligned to GRCh37-lite genome-plus-junctions reference [1] using BWA version 0.5.7 [2]. This reference is a combination of GRCh37-lite assembly and exon-exon junction sequences with coordinates defined based on transcripts in Ensembl (v61), Refseq and known genes from the UCSC genome browser (both were downloaded from UCSC in November 2011; The GRCh37-lite assembly is available at http://www.bcgsc.ca/downloads/genomes/9606/hg19/1000genomes/bwa_ind/genome). BWA "aln" and "sampe" were run with default parameters, except for the inclusion of  the (-s) option to disable the Smith-Waterman alignment, which is unsuitable forinsert size distribution in paired-end RNA-Seq data. Finally, reads failing the Illumina chastity filter are flagged with a custom script, and duplicated reads were flagged with Picard Tools (version 1.31). After the alignment, the junction-aligned reads that mapped to exon-exon junctions were repositioned to the genome as large-gapped alignments and tagged with "ZJ:Z" by JAGuaR (version 2.0).

Reference
[1] Butterfield et al. (2014) JAGuaR: Junction Alignments to Genome for RNA-seq Reads. PLoS ONE 9(7): e102398. doi: 10.1371/journal.pone.0102398
[2] Li, H., and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760