Fig. 2

Chimeric transcript detection and characterization by R-SAP. Assembled contigs (black box) representing chimeric transcripts will produce discrete or fragmented alignments (blue and grey boxes) when mapped to the reference genome. It will result in the alignment structure where fragments of the assembled contigs will map to the genomic locations (e.g. chromosome A and chromosome B) underlying the fusion-gene formation. This structure is also called ‘split-mapping’ of the contig. R-SAP detects split-mapping and then compares the alignment coordinate of each fragment with the genomic coordinates of the known reference transcripts (shown in green boxes). Based on the fusion-point mapping (vertical orange bar on the top), R-SAP can determine the transcript regions (such as CDS or UTRs) that are involved in the gene-fusion