Repository navigation
Fusion Gene Analysis #498
Description
Hi,
Thanks for creating this wonderful tool. I had a question regarding the fusion gene/isoform mode. I was following the tutorial mentioned in #433 but am having trouble getting it to work. Do you have an updated version of the tutorial since you mentioned its a preliminary version?
As I mentioned in the other issue, I think it is due to the fact that JAFFAL identified multiple fusions between two genes that have different breakpoints and thus the getFusionTxRange function computes multiple values for scoreNum. Would another approach be to generate custom names for each fusion transcript and then extract the sequence information and generate an annotation for the transcripts in order to avoid the issue arising from having different breakpoints for the same transcript?
Activity
cying111 commentedon Apr 15, 2026
Hi @mpizzagalli777 , sorry for getting back so lately.
My feeling is that if there are multiple breakpoints, it shouldn't be a problem. One fix is probably that to collapse your fusion genes from the same 2 set of genes together, if they are only different in breakpoints, i.e., exactly the same 2 genes.
Then later on when using bambu, if reads exist for multiple breakpoints, novel fusion transcripts will be identified by bambu.
Hope this is still relevant.
Thank you and feel free to let us know if you need our help with the above steps.
Regards,
Ying