Fig. 3From: De novo assembly and characterization of breast cancer transcriptomes identifies large numbers of novel fusion-gene transcripts of potential functional significanceRe-confirmation of chimeric transcripts. In order to remove chimeric transcripts resulting from potential mis-assemblies, we looked for the support for chimeric transcripts (green-orange boxes) in the original RNA-Seq reads (black boxes). RNA-Seq reads were mapped to the chimeric transcripts and reads spanning the fusion-junction (vertical red box) were counted. Reads were also mapped to the reference genome and the occurrence of mate-pairs mapping to the genomic locations underlying the gene-fusions confirmed. We consider a chimeric transcript as ‘confirmed’ if there are at least two reads supporting the fusion-junction and at least two mate pairs supporting the genomic alignment of the chimeric transcriptBack to article page