TanZhengTang

> Thanks, and yes, that happens periodically. You can visit the AA readme and follow the link to get another license. For the academic license, I believe you can obtain...

Yes,I updated the license and ran AA again.In this time,I got 3 amplicons from gbm39-wgs data.But I don't understand the difference in amplicon and ecDNA.Is the ecDNA part of amplicon...

Thanks!I have used the AmpliconClassifier to produce one of my amplicon status,according to output of [gbm39_ec_amplicon_calssifier_amplicon_classification_profiles.txt](https://github.com/virajbdeshpande/AmpliconArchitect/files/5456516/gbm39_ec_amplicon_calssifier_amplicon_classification_profiles.txt) ,this amplicon is circular with a probability of produced by ecDNA?

I used bwa 0.7.17 and all the log content: INFO:root:Commandline: /home/tang/tools/AmpliconArchitect/src/AmpliconArchitect.py --bed ../NCI-H716_AA_CNV_SEEDS.bed --bam ../NCI-H716_hg38_align_sort_rmdup.bam --downsample 0 --out NCI-H716_ecDNA --ref GRCh38 INFO:root:AmpliconArchitect version 1.2 INFO:root:#TIME 7.035 Loading libraries and reference...

According your advice,I checked my bam file,and found a mistake that I used double R1.fq file when I aligned. I'm a newbie in this field,I have read a bit of...

I get it. But I’m curious if there is an experimental method to isolate ecDNA for analysis?In this way if we can get the complete structure of ecDNA? Thank you...

> Hi, > > The regions identified by CNVkit are filtered by the AA script 'amplified_intervals.py', to remove regions that are too small to be candidate AA amplicons, too low...