File S1 - JAGuaR: Junction Alignments to Genome for RNA-Seq Reads

Table S1, Example Transcript Model. Figure S1, JAGuaR first requires the reference genome of interest and a transcript model in order to build the reference of the genome sequence and exon junctions. Figure S2, Based on a transcript model (Table S1), JAGuaR assesses each exon-exon junction of all available transcripts. Figure S3, SNV concordance between tools for one read set (Sample 1). Figure S4, SNV concordance between tools for one read set (Sample 3). Table S3, SNV Comparison to running of BWA-MEM alone. Figure S5, Comparison of JAGuaR+BWA-MEM/BWA-MEM exon start or stop coverage fraction. Text S1, Parameters used for Flux Simulator.
(DOCX)