Jens Luebeck

Hi, The amplicons reported by AA are general focal amplifications, which can be created by many mechanisms including ecDNA. If you would like to classify the status of these amplicons...

Hi, Yes the amplicon recieved "Positive" in the ecDNA+ column, and thus it is predicted that amplicon1 contains ecDNA. You can use --extract_genes to get a bed file specifying the...

Hi Brian, Sorry for the delayed response. Thanks for reaching out about this. I am curious if this data you are running AA on is paired-end WGS data? AA currently...

Hi, Thank you for your interest. Unfortunately WGBS/ATAC are not suitable inputs for AA; only paired-end WGS is usable currently. I agree that you will likely identify concordant CNV focal...

@papenfuss, there is a more active discussion about this issue here: https://github.com/jluebeck/PrepareAA/issues/17#issue-956365839. Please feel free to email me any log files and commands used to run AA and I will...

Hi, I have not seen this error before. Could you please upload any log files produced by AA. Could you also clarify which aligner was used to generate the BAM...

Hi, I believe the issue is that somehow NaN is assigned for the mean read_length or max_insert size. Can you please try the following. 1. Always remove temporary results from...

Hi ZhengTang, No problem. With NGS data alone, we can only make bioinformatic predictions of ecDNA regions given breakpoint graphs. The confidence of those predictions increases when FISH data or...

Hi, Some groups have had success isolating ecDNA using the Circle-Seq technique, for example in the following publications: https://www.nature.com/articles/s41588-019-0547-z https://www.nature.com/articles/s41588-020-0678-2 Best regards, Jens

Hi, We have not tested this before. However, because AA uses discordant read pairs to identify the presence of junctions (which are refined by split-reads), the absence of discordant read...