I understand that Cufflinks can report FPKM on novel transcripts (different isoforms) if using proper parameters, but I wonder whether cufflinks is able to report FPKM on chimeric transcripts/gene fusions between different genes? for example, if a fusion happens between exon1 of gene1 and exon5-6 of gene2, would cufflinks be able to report an isoform (the fusion) in some format as below (in the transcripts.gtf):
chr_gene1 gene1_exon1_start gene1_exon1_end gene1_exon1_fpkm chr_gene2 gene2_exon5_start gene2_exon5_end gene2_exon5_fpkm chr_gene2 gene2_exon6_start gene2_exon6_end gene2_exon6_fpkm
Based on a test case I ran, I don't see cufflinks reporting the fusion transcripts..., but I wonder whether it's because I was not using the right parameters or cufflinks never does that.. Please advise.