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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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When I run decoil-viz, I meet the error below:
```
processing file: template.Rmd
|........................ | 54% [draw_amplicons] R[write to console]:
Quitting fro…
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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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If I have this output from decoil, which files can I use to visualise any potential ecDNA. The manuscript mentions using gGnome
clean.vcf
config.json
coverage.bw
fragments_clean_1.bed
fragments_c…
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I've managed to get decoil to run with my data and produce all the right files but I am missing the summary.txt file
This file was produced with the test data but not with my own data.
(I used sing…
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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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Hi! I'm currently facing an issue while running Decoil: after going through various samples, I've encountered a persistent problem with one specific sample. The process seems to be stuck at a particul…
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Hi there,
I used the end-to-end wrapper to process my data, but I didn't get any ecDNA. So, I want to check the steps one by one.
I reran the data following the log file generated by AmpliconSuite-p…
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Dear Dr.Yang,
Thanks for your useful tool. I have a question about the cutsites.py script that why the value of flag 83 is reference_start rather than reference_end? It seems that the "163: 'refe…
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Hi,
I have multiple 30X WGS data and want to try AA on it. As mentioned in other issues, 30X is too large for AA and downsampling is recommended. But I'm not sure which one is the right way for downs…