Multiple insertions on the same scaffold

[SergeWielhouwer]

Dear Vanja,

Thank you for developing TC-hunter. I have been trying out TC-hunter for quite some time now with simulated data with success. The resulting Circlize and IGV plots really help to understand the results better 😄.

I was wondering if you have any idea how multiple insertion sites on the same scaffold could possibly be detected by this tool by potentially updating the code or any new tool? In your paper, the following is stated "At the moment, TC-hunter does not distinguish between multiple IS within the same scaffold. Nonetheless, inspecting the graphical aids, the chimeric reads and discordant read pairs may hint of these multiple events. We expect to implement solutions to these pitfalls in future versions of TC-hunter." which I encountered as the software would crash (in my case during createOutput.py).

Do you have any thoughts on this?

Best regards,

Serge