Jens Luebeck

Awesome - good luck with the analyses and let us know if you have any questions. We have wrapped the data pre-processing and post-processing (amplicon classification) steps into a wrapper...

Hi Alex, You can use your own fasta file to generate the BAM, without any modifications to the AA data_repo, provided it is some version of hg19, GRCh37, GRCh38/hg38, or...

Hi Alex, that's correct!

Hi, Can you clarify if it was KT22, KT26, KT31 , KT32, KT33, KT34 which you found to be the same, or if it those samples were different? Perhaps, would...

@dlaehnemann, if you had not already seen, please see the bioconda install for AmpliconSuite-pipeline, which includes AmpliconArchitect. https://github.com/AmpliconSuite/AmpliconSuite-pipeline#option-b-install-with-conda-or-mamba ```bash conda install -c bioconda -c mosek ampliconsuite mosek wget https://raw.githubusercontent.com/AmpliconSuite/AmpliconSuite-pipeline/bioconda/install.sh source...

Thanks David*, these pointers are great. I have added a dedicated license file with the UCSD license pending in the open PR for @virajbdeshpande to merge so that it is...

Hi Viraj, After discussing with Zhang in a separate thread, I believe this is an issue caused by the cycle_visualization tool not supporting hg38 output from my fork. I have...

Hi Tangzheng, At the moment, the bed file input for amplified_intervals.py requires the following format: `chr start stop arbitrary_field estimated_CN` Which is the output format for readDepth. A bed file...

Hi, it appears AA did not finish correctly. We would expect three amplicons of output. Could you share the gbm39-ec.log file? One suggestion, did you remove all files created by...

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 another...