Jens Luebeck

Hi, Thanks for reaching out with this query. If the sample does not have ecDNA, then a result that does not contain any ecDNA is expected. I am happy to...

Thanks Jian, do you have a directory containing the AA output files? `C8_merged_AA_results/`. That would be helpful to see. It's hard to know how will this will work even on...

Thanks you for sending. I don't see any errors. One question is which aligner was used and what parameters were used for alignment. Can you provide the header of the...

Thanks, I believe the most likely reason is that either there is no ecDNA or it is below the detection threshold. Other issues related to the use of scWGS may...

Looks good - you may want to set `--run_AA --run_AC` if you are planning to launch AA and AC after.

For some cancer types (e.g. GBM) this rate is expected. I would be happy to look at any outputs or log files you would like to share to check for...

Strange - it is a Google-managed account and is able to get other messages. Perhaps can you try sending from a different email? It's also possible it does not like...

Thanks for sending the tumor-only files. I reviewed the files and the outputs look to be in order. I did not see any obvious bugs. In a small number of...

Yes, that should be an acceptable control. The files previously sent did not indicate a version of AmpliconSuite-pipeline, but please consider updating to latest (1.0.0): https://github.com/AmpliconSuite/AmpliconSuite-pipeline

Hi, Yes - we can add an argument to make this choice possible. In the meantime though, one can make a small modification to the docker runscript for AA (or...