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Hello,
I want to use treeWAS for Bacterial GWAS, and my data is in the form of SNPs and gene presence /absence, but when I run the program I get the (Error in tree.reconstruct(genotype, method = …
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Hello,
I am using pangene to determine the presence and absence of genes across various populations of my model species.
As recommended I created a pan-gene library and used miniprot to align prote…
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Is the Diamond output file the annotation of the entire bin or is it the annotation of specific genes that checkm2 considers important for things like completeness/contamination calculations?
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I've been running Roary in order to use the presence/absence tables as input for training ML models (to identify sub-species groups based on shared genomic features). As I don't really care if genes a…
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Hello,
Thank you for this tool. I am attempting to use this to do power calculations for pan-genome GWAS. These are the commands I have run:
python3 ./scripts/annotate_nodes_newick.py --input_…
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Hi Dr Horesh,
Firstly, thanks for developing this tool, it’s a really neat way of categorisating the accessory genome, and very useful and usable.
When first trying out the script, I noticed tha…
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Currently this function splits lines where the same variant has multiple annotations (e.g. overlapping genes)
This function deals with lines such as Coding SNP ... > A,G
Create a new function to:
…
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Hi all,
In brief, I am using `anvi-push` to push pangenomic data to `anviserver` and I get this error:
`Anvio Server Error: module 'anvio.dbops' has no attribute 'TablesForCollections'`
The p…
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Hi,
To render more conterable roary and the scripts associated, it is possible to add an option of "output directory" or "output path" to choose where saves the files produces by `roary_plots.py` ?…
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e.g. the polar auxin transport pathway in rice has few reactions that are not necessarily mediated by involvement of gene product. such as the direct IAA transport (export and import)--a diffusion re…