I want to make sure that I am understanding the results from BreakDancer correctly when it comes to translocations. In the manual it says the following:
1 10000 10+0- 2 20000 7+10- CTX -296 99 10 tB|10 1.00 BreakDancerMax-0.0.1 t1
With the following explanation: inter-chromosomal translocation that starts from chr1:10000 and goes into chr2:20000 with 10 supporting read pairs from the library tB and a confidence score of 99.
Does this mean that only the breakpoints chr1:10000 and chr2:20000 are involved in the CTX ?
Or does this mean that from chr1:10000 onwards (to the end) translocated with chr2:20000 onwards? I.e. That chr1 "was cut at" 10000 and chr2 "was cut at " 20000 and then the two cut parts are what translocated.
If the example was ITX,
1 10000 10+0- 2 20000 7+10- ITX -296 99 10 tB|10 1.00 BreakDancerMax-0.0.1 t1
Would this mean that the chr1 was "cut" at 10000 and "cut" at 20000 then the region from 10000-20000 moved to the 20000-30000 and the region from 20000-30000 moved to 10000-20000?
I looked to see if there were other questions similar to mine, and I could not find one. I found an answer that referred to the BreakDancer Old ReadMe which I am using.
Thank you for your help.