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Dear Maintainers,
I got this error when trying to run ampliconsuite inside nextflow, so I am unsure if this occurs because of nextflow or maybe the issue arises on your side.
I also tested the con…
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v0.4.13
The coordinate in cycle file is, for example,
chr1 100 *500*
however, in the eccDNA_x_intervals.bed output file, it becomes
chr1 100 **501**
for other outputs, like BFB_x_intervals.…
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Hi,
when I call CNVs using CNVkit, need to consider sample purity and ploidy to caculate absolute copy number?
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Dear Dr.Viraj
I am trying to use AA for following your work to produce ecDNA data.When I run the amplified_intervals.py to produce the bed file which AA need,bad things happend.
my code is:
pyt…
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I have some samples -only tumour, no any normal samples as control, and here is my code for these pipeline, it's OK?
python3 /share/home/luoylLab/zengyuchen/biosoft/AmpliconSuite-pipeline/PrepareAA…
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### Description of the bug
Hi!
I'm running the pipeline with the following pipeline:
```
nextflow run nf-core/circdna \
-r 1.0.4 \
-profile docker \
-resume \
--max_cpus 9 \
--max_memory …
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Dear,
I have used AmpliconArchitect to calculate ecDNA,and I got the output store in {sample}_circle.txt, It is look like this:
> ......
> Segment 39 chr17 74733453 75044078
> Segment 40 chr17 7…
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Hi,
It's really interesting tool to identify circle DNA from DNAseq data. But, recently, we are considered with the variety of circle DNA length and length of insenrtion of reads, which would influen…
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Finally got AA setup on a pretty beefy server and when i run the docker script i notice that the results are written as root. This may be a silly question but is there a way that the results can be wr…
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Hi,
I'm running PrepareAA with sorted .bam file and in the summary file I do obtain 1 amplicon, however, the cycles.txt and graph.txt are empty (I didn't get the SV view file). I was running the Pr…