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Hello,
I ran roary and got the necessary files. I downloaded the roary.plots code in a "roary_plots.py" file. I tried running the next line of code:
`python roary_plots.py core_gene_alignment.nw…
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Hi there,
For some background, I am trying to build a presence/absence matrix of genes from >500 diverse genomes. But I find that eggnog-mapper does not always give me the gene name even though I …
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Hi Gerry,
I get that Panstripe's main goal is to model the gene exchange rates, but would it be straightforward to get an idea of the function of the exchanged genes? I'm thinking of listing annota…
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Hi Ola,
I'm working with a large number single-cell amplified genomes, i.e. the individual assemblies are incomplete, ranging from ~30%-95% estimated completeness. This means that I do get reliable…
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Using:
CARD
ResFinder
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Hello,
On the roary website it mentions that panx can be used to visualize the data. I'm trying to load data into panx like the panx website says but the roary output is not recognized. I'm follo…
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Hi Zhichao,
In my current MAG, there is no NorB and C genes (they are responsible for the step "NO ---> N2O", dash lines represent no Nor genes in the MAG, as shown in the pdf file). Is there any o…
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This relates to cases where a study contains a sample which appears to be part of a genetic profile, but the sample is not present in data_gene_matrix.txt, or the gene panel id value is 'NA' or missin…
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Hi @tseemann, I see you posting often on this github, so thought I'd ask!
I'm having some issues getting a core genome alignment of around 300 full-length _E.coli_ sequences w/ ROARY.
The prog…
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The Query page contains a dropdown menu to select a gene set, which is used to query multiple genes specific for a specific pathway. The contents of this dropdown menu is hardcoded in a Typescript fil…