error in chaining fusion transcripts about cdna_cupcake

[Magdoll]

Hi @fantastycrane ,

This is a deliberate error thrown to notify the user that the script cannot make an unambiguous decision in chaining fusion transcripts across samples.

In the case you provided, PBfusion.114 and PBfusion.210 are two fusions that each consist of two single-exon segments and these two single-exon segments overlap. So, the script cannot make a decision in this case for chaining because there are multiple candidates to chain with.

There is no easy solution at this point. The purpose of the script throwing a warning is to ask the user to manually examine and remove these conflicts. You would either remove one of the two fusions or create a new fusion that represents the two fusions in some manner.