Figure 1.

RNA-seq realignment schematic. A spliced read aligner is used to identify sample specific novel splice junctions that are used to generate a splice junction index. Read 1 and read2 from each read pair are independently mapped to the genome and splice junction index using a contiguous read aligner. Low quality alignments are removed, the genomic and splice junction alignments are merged and the read pairs are resolved using an empirically determined fragment size distribution.