about compare with short read SV in paper

[charliechen912ilovbash]

Hi, Could you describe a little bit about how you compare with short read sequencing detected SV in the paper? Like what is the margin (e.g. 20bp) to decide two breakpoint are closed enough to consider as the same SV. Thanks

[friend1ws]

In the paper, I used three categories; Detected, Partially detected, Not detected. Detected: Both the breakpoints and their directions match an SV detected by the short-read sequence platform within the margin of 30bp. Partially detected: One of the breakpoints matches an SV detected by the short-read sequence platform within the margin of 50bp. This applies often to LINE1 transduction, where they are usually identified as translocation in the short-read platform whereas it is identified as an insertion in the long-read. Not detected: Otherwise.

[charliechen912ilovbash]

Thanks for answering. So in the Figure 2b, the red parts (detected by both short and long read) are Detected + Partially detected ?

[friend1ws]

Thank you! I have never been asked this question by reviewers. But you are right. The red parts in Figure2b are Detected + Partially detected.

[charliechen912ilovbash]

I understood, thank you very much for answering!