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Hi, good day. i have the following problems but my tormes format is generated but with errors.
error reported on command line
"WARNING: Core gene alignment tree was not generated during pangenome …
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Currently outputs a pangenome matrix file with a dodgy name (missing /?)
Currently outputs a directory for every gene found in any sample - make this one for everything.
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Hello,Professor
I have two assembly genome of two species. I want to construct a graph from the two genome using PGGB. I firstly combine the two genome into a input.fa ,then index the input.fa , fina…
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Hi, on https://www.mbru.ac.ae/the-arab-pangenome-reference/ it is not possible to download the assemblies. As soon as I click on links to download APR Nuclear or APR Mitochondrial assemblies, I get a …
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I have been trying to use the higher-sensitivity branch for running wfmash alignments on my data. The code seems to be much faster than the master for producing the alignments although gives me an err…
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## The need
To annotate pan-genome genes, the user is encouraged to export from an existing pan-genome database via `anvi-get-sequences-for-gene-calls -g` and then annotate the genes via their own …
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Can you provide a detailed explanation on how to run this process? I am a beginner and don't quite understand. Thank you very much
tttxd updated
3 months ago
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Hello to the pagoo team,
First, my congratulations on the great work made on the development of pagoo R library.
The main question I want to put in this forum is in the following:
1) Is ther…
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This is a followup to the closed issue as noted in #291, which can be worked around using the [nf-core pangenome workflow](http://nf-co.re/pangenome/). I have separately confirmed this using the same…
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Hello Coinfinder Developers,
I've been using Coinfinder to analyze my pangenome data, but I've encountered some issues with the output files, specifically with generating certain expected files lik…