Jens Luebeck

Issues addressed in AmpliconSuite-pipeline v1.3.3

Hi, Unfortunately, this technique for manual combinations of paths/cycles mentioned in the AA README is now deprecated. We are a very small team working on this tool and we did...

Hi Weijia, The advice about more than >50 entries in the seeds file applies to the AA_CNV_SEEDS.bed file. It would appear the problem though is the `--cnsize_min` argument. 500bp is...

Hi Weijia, Are the samples producing any outputs in log files or stdout? If there is no logging output then there may be a problem. We've found that using anything...

Hi, Your GBM39 test results appear correct. An empty seeds bed file implies there are no candidate regions of focal amplification that are detected in those samples. There is also...

Hi, Your outputs appear to be correct. Keep in mind that focal amplifications almost exclusively occur in cancer and pre-cancer samples. If you are providing samples from healthy patients to...

Hi Yingzhou, AA is designed to detect large (>10kbp), focally amplified ecDNA. If the eccDNA in question are smaller, or if they are not amplified then AA will very likely...