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version:
ampliconsuite 1.3.2
mosek 10.1.31
command:
AmpliconSuite-pipeline.py -s XXX -t 12 --bam ../bam/XX.bam --run_AA --run_AC --ref hg38
Report error when r…
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Repro:
Running AS-p GroupedAnalysis mode via registry.hub.docker.com/jluebeck/prepareaa:v1.3.3: `python /home/programs/AmpliconSuite-pipeline-master/GroupedAnalysisAmpSuite.py --input input_file.tx…
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Dear AmpliconArchitect Team,
under which license is AmpliconArchitect available?
I would like to put your software into bioconda to make it available for a broader range of users.
However, I woul…
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Dear AmpliconArchitect Team,
I would like to ask you few questions regarding the samples you used in the manuscript.
I used same WGS data from BioProject (accession number: PRJNA437014, only KT sa…
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Dear AmpliconSuite Developers,
First of all, thank you for developing such a great software that provides a lot of convenience for ecDNA research. I encountered a little difficulty when trying to a…
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Hi,
I Ran the AS-pipeline for the bam that my colleague has run by AA(1.2_r2) and AC (0.4.13) but got different results, then I considered it as a version problem.
So, I install the AA and AC as …
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Hi authors,
Thank you for your wonderful tool. I applied AmpliconArchitect for identification and AmpliconClassifier for classification of ecDNAs in resistance and vehicle models. I obtained large …
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Hi,
I have run the AmpliconArchitect with following command "python2 AmpliconArchitect.py --ref None --downsample 10 --bed WGS000100002tumor_AACNVbed.bed --bam WGS000100002tumor.dup.reali…
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Dear Viraj,
It is me again. I have manage to skip the `ZeroDivisionError` by filtering out the reads with low mapping quality. I am writting you to ask if you could provide some lines in the descri…
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Hi,I've ran AA with bam file (WGS) with the code below and error message shown as follow:
AmpliconArchitect/src/AmpliconArchitect.py
--bed seed_50kb.bed
--bam pe_q0_redup.bam
--sensitivems Fal…