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May I know what is Mosek used for in the application? Does it have to be Mosek 8? Which command(s) invoke Mosek and how do I check I am actually using Mosek in the output log or similar file?
Thank…
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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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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
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Hi,
I have two queries regarding the `coverage.stats` file that gets updated in the `data_repo` folder everytime we run AmpliconArchitect for a particular sample -
1. what are the different column…
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So I've downloaded the GRCh38 repo and I am using the docker image. When I run my command I get the error below:
root@chimera:/home/joshi/sandbox# $AA --bed /home/joshi/sandbox/seed.bed --bam /home…
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Hello,
I am trying to utilize the AmpliconArchitect docker image for a workflow in an instance of the google cloud platform. In my workflow, I have written the following based on what I saw in the …
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hi~ sir:
my bams all are more than 30X wiht B37。
Is AmpliconArchitect very slow when run on such large bam?
Waiting for your reply,thanks。
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Dear Viraj,
I am Iñigo Prada-Luengo. The developer behind [Circle-Map](https://github.com/iprada/Circle-Map). I have really enjoyed reading your manuscript and the algorithmic ideas behind Amplicon…
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I ran AA, while the summary said it had 30 amplicons, only one plot (for amplicon1) was made.
And the log said,
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[root:INFO] #TIME 151754.862 Reconstructing amplicon2
[root:WARNING] dnlists…