One of my downstream analyses requires to know the orientation of the breakpoints. For example, for INV, it needs to know whether it is head-to-head ("++") or tail-to-tail ("--"). And there can 4 possibilities for ITX/CTX: +-, ++, -+, and --. Can I get this information from BreakDancer results? There are columns named "Orientation1" and "Orientation2" which the manual says are the number of reads mapped on + and - strands. Is it something that can be used to infer the SV orientation described above?
xyw1
commented
5 years ago
One of my downstream analyses requires to know the orientation of the breakpoints. For example, for INV, it needs to know whether it is head-to-head ("++") or tail-to-tail ("--"). And there can 4 possibilities for ITX/CTX: +-, ++, -+, and --. Can I get this information from BreakDancer results? There are columns named "Orientation1" and "Orientation2" which the manual says are the number of reads mapped on + and - strands. Is it something that can be used to infer the SV orientation described above?