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Hi,thank you for your work. I tried to use prepareAA accompanied with AA to detect ecDNA on mouse but found there calls a error when I entered the command line.
```
(HRenv) [renhb@localhost ~]$ p…
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文献描绘的ecDNA的概念大概应该是:高度扩增的,携带有oncogenes的环状DNA ,不一定要特别大。据我了解circle-Map仅限于找到拆分的两个junction位点,请问你大概用的什么原理找的ecDNA呢
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## Command
python3 PrepareAA.py -s R18008004LD01-A130017-1 -t 4 --cnvkit_dir /xxxj/software/cnvkit/cnvkit.py --bam R18008004LD01-A130017-1.bam --ref GRCh38 -o R18008004LD01-A130017-1_AA_OUT_10x.expan…
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GDC: https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/
- features we'd like to support: snv, indel, structural variants, extra chromosomal dna
- create ta…
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Hi, I am trying to detect ecDNAs from my circle-seq data,is AA suitable for that?
and I am going to use prepareAA and CNVkit to get the CNV bed files which will be feeded to AA.
If not, could you gi…
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I already use `--AA_runmode` to stop create the output for SV visualization. But still show process of SV View and stuck here for 5days. :
```
[MOSEK:INFO] Beginning MOSEK call
[root:INFO] …
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Hi:
When I run run_aa_docker.sh, I encountered the following error:
![4](https://user-images.githubusercontent.com/54090957/110727288-e8882680-8255-11eb-9cd7-6ec9a593eda5.png)
Then I checked …
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In the AmpliconClassifier documentation is detailed, that only cyclic amplicons can be classified into BFB or ecDNAs.
However, in my analysis, I noticed that some were classified as Complex, but the…
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### Description of the bug
Hi! I'm using nf-core/circdna with the following configuration:
```
nextflow run nf-core/circdna \
-r 1.0.4 \
-profile docker \
-resume \
--max_cpus 9 \
--max_memo…
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Dear Viraj,,
I am trying to run AA for my data focus on cancer samples. However, when I runned amplified_intervals.py, no output was there in the bed file, my code is:
/public/software/aaconda…