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Dear Viraj,
My reaearch are mainly focused on small ruminants, like sheep and goat. I hope to know that is it possible to use AmpliconArchitect on these species? Will you give it such features in th…
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Hi sir,
here is my coding
` python /data1/work/software/AmpliconArchitect/src/AmpliconArchitect.py --bam bam/YX150000261T.final.bam --bed gain.bed --out AA_out`
it keeps running for 60h but no outp…
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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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Hello,
In the "Creating the BAM file" section of the guide, it is mentioned that BAM files from Isaac are allowed. Are there any restrictions on this or settings to change? We have a number of Issa…
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Hi,
I am running AA by using PrepareAA.py, and my command is:
/scratch/xiaomingzhong/helpOther/lisui/tools/PrepareAA/PrepareAA.py -s aatest -t 8 --cnvkit_dir ~/anaconda3/envs/aa/bin/cnvkit.py --…
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Hi,I tried run AA with the outputs of AApipeline many times.And I always stuck at "Optimizing graph copy number flow". And this is the error.
![image](https://user-images.githubusercontent.com/12260…
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Hi Jens,
After running AmpliconArchitect, I got results like following:
Cycle=66;Copy_count=0.0929550935359;Segments=13+,83-,105+,139-,0-,0+.
I don't know how to interpret this result.
Cou…
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Hello,
Firstly thank you for a very useful and interesting software package! I have a quick question about the "coverage.stats" file that is generated as part of the AmpliconArchitect pipeline. As …
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I can't seem to get AA running after pulling the latest image and cloning from github, AA_DATA_REPO is set as:
`$echo $AA_DATA_REPO`
`/home/Genomes/aa_data_repo`
Output after execution command:…
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Dear author,
I'm running AmpliconArchitect on my WGS data. It ran completely but got a warning, and the result only showed one Amplicon on chr1:
> [root:INFO] Commandline: /home/heng/ZhangHeng/A…