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When I run the last step from your workshop at https://github.com/chrisquince/CopenhagenWorkshop/blob/master/Tutorials/StrainResolution.md
I repeatedly got **IndexError**s:
`/Volumes//DESMAN//d…
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Hi,
I don't know why, my roary run seemed to have stopped too soon after producing gene_presence_absence.Rtab file. Is there a way to continue the run from this point?
This is the command that I…
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Hello, I am trying to run roary to get a core genome alignment of ~2500 salmonella genomes annotated with prokka, and I am unable to get the final outputs even though the cluster (PBS) returns a succe…
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# Description
Basic model curation by reviewing GPR, confidence level, and metabolic reactions.
# Solution
- OR and AND annotations were corrected.
- New functions and genes were added.
- Confid…
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Dear Jon,
Thanks for your suggestion for setting up the funannotate in our HPC environment.
It works well with the parameters of --transcript_evidence and --protein_evidence.
But when --rna_…
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Hi
I ran Roary on a set of B. longum genomes from NCBI (see list) and the accessory_binary_genes.fa file produced only had A and Cs.
Was wondering if this make sense?
[Bifidobacterium_longum…
ghost updated
7 years ago
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Hi, I am analyzing 28 bacterial genomes using Roary.
And the summary statistics is as follow:
Ortholog class Definition Count
Core genes (99%
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Hello! I am trying to use Roary to make a core-genome alignment for around 900 isolates of Pseudomonas aeruginosa. For each isolate I have an assembled genome annotated with prokka. I did some test ru…
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Remove enforcing of the columns "Non-unique gene name" and "Annotation" in the output. Some users might have input file with only a single identifier column (Gene ID) before sample info starts, and wa…
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Hello,
Great job on the program - looks very promising!
Unfortunately, I am having some issues implementing treeWAS using ClonalFrameML output. I can load the data just fine using the read.CFML(…