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Hi, I had some problems extracting data from interactive output pages.
I successfully ran the query module to analyze the novelty of my BGCs (more than 1000), and here are the command I used:
`bi…
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Hi,
I am building a pangenome of 7 genomes and trying to see the impact of identity thresholds on the pangenome estimations. When I run ggCaller with the following command:
ggcaller --refs input.t…
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Hi Guys,
Thank you for such a great software!
I am trying to annotate 39 plant accessions each about 4GB and I am only able to run a GPU node of my cluster for a maximum of 4 days. Unfortunately…
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Hello,
I'm wondering what the difference between the clusters and clusters_merged HMMs for each EPS operon are? Are one set of HMMs the original HMM and the other set the iterated version?
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Hello,
I downloaded BiG-SCAPE from here: https://github.com/medema-group/BiG-SCAPE/archive/refs/tags/v1.1.5.zip
When I try to run for only three genomes (antiSMASH outputs) I can run it without …
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@hammer, I put together a [notebook](https://github.com/hammerlab/t-cell-relation-extraction/blob/04fe235bdbf78d3f5b93675a4ca13faea6e41500/pm_subtype_protein_relations/entity_linking/eda-word2vec.ipyn…
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I encountered a `TypeError` when trying to run `ggCaller` from source following the example provided in the documentation. The error message indicates an issue with the `set_axis` method from the pand…
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Please provide as much information as you can:
* **Suggested term label:**
mycofactocin-coupled metabolic process
* **Definition (free text)**
The chemical reactions and pathways performed by…
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I ran BiG-SCAPE on the following MiBIG clusters: BGC0000187, BGC0000194 through BGC0000198, BGC0000213, BGC0000220, BGC0000247, BGC0000269, BGC0000275, BGC0001851, BGC0002045 which all appear as type …
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Hi, I wrote about another step. I successfully finished others so thank you for your help!
Little question about step `syn`. I have a gff3 file from the _Augustus_ , but when I run the command:
…