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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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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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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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Hello,I meet a question when I run AA for getting data.
The AmpliconArchitect version is 1.2
my command:
python /home/tang/tools/AmpliconArchitect/src/AmpliconArchitect.py --bed ../NCI-H716_…
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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…
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After calling CNVs by ReadDepth (reads mapped to hg38), I tried to get seed intervals by running `amplified_intervals.py`. But I got errors as bellow (run program on a HPC server):
_WARNING:root:#TIM…
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Hi Viraj,
Thanks for your work in AA. Do you know what happened about this error? Thanks for your help.
$]cat test_out.bed
7 54700000 54950000 30.0 /dfs3/weil21-lab/yac7/data/test.bed
#####…
YaCui updated
4 years ago