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Similar to #11 I'd like to make my decoil ecDNA calls more conservative. But most of my samples have ~25-30x and I don't want to downsample them and loose information unnecessarily.
With default…
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Same goes for private projects made public.
For example - when I replace Contino with a new copy of Contino on a public project, the following happens:
```
# init
Projects 5
Samples 358
Foca…
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There are two ecDNAs in AC's annotated_cycles file, but ecDNA_counts.tsv only gives one, and the bed file of this ecDNA is a combination of the two ecDNAs in the annotated_cycles file, so which one sh…
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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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I am struggling to completely understand the differences of the outputs in AA and AC and how to translate this to presenting the results of the analysis:
If I have an individual sample which appears …
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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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Hi,
I was wondering if decoil currently supports the t2t reference genome?
I used decoil on the same sample with the grch38 and then the t2t reference genome. The grch38 reference gave the expe…
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Hi, I have read your impressive work "Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma Nat Genet (2020)." But I didn't find some explicit criteria to distinguish ecDNA…
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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, 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…