Hi,

I am trying to use bambu to identify novel isoforms in my long read RNAseq data (Pacbio Kinnex). In the attached IGV screen shot, the top junction is the normal junction with 162 reads and the bottom one is the "abnormal" junction with 40 reads (12bp away from the normal splice site). This should create a novel isoform but bambu wasn't able to call a novel isoform in this gene.

We have done short read RNAseq on the same sample to confirm that this abnormal splice site is real. I am wondering why bambu wasn't able to call this. I have tried min.exonDistance = 1 but it doesn't help.

I am using the newest version of bambu (installed from the github repo)

Thanks for the help!
Laur