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Old 02-22-2018, 07:52 AM   #1
DNAmethylome
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Default Can Cufflinks report chimeric transcripts/fusions?

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.

Thanks!
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Old 02-22-2018, 12:11 PM   #2
DNAmethylome
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Can someone help me on this question?

Thank you very much!
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Old 02-28-2018, 05:22 AM   #3
l_zembek
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You may be more interested in TopHat fusion for this purpose:
https://ccb.jhu.edu/software/tophat/fusion_index.shtml
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