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Dear all,
I have been having the following issue when installing panX. I followed the steps as in the site and used miniconda as indicated.
`Traceback (most recent call last):
File "./panX.py…
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Just an issue to collect any relevant papers. For example, there's a whole Genome Biology issue on graph genomes at
https://www.biomedcentral.com/collections/graphgenomes (also see "Pangenome Graph…
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$query_pan_genome -a difference --input_set_one 1.gff,2.gff --input_set_two 3.gff,4.gff,5.gff
Error: Cant access the groups file: clustered_proteins
Usage: query_pan_genome [options] *.gff
Perfor…
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Hello,
I was curious to know how annotation is handled after 2 dbg graphs are merged using VariMerge? Is there an annotation tool (for bacteria) that the authors of this software would recommend al…
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(panX) anna@Anna-PC:~/work/pan-genome-analysis$ sudo sh run-TestSet.sh
Traceback (most recent call last):
File "./panX.py", line 6, in
from pangenome_computation import pangenome
File "/h…
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Hello
I am teaching myself how to run panX using TestSet. Here is the command I run exactly following the instructions.
./panX.py -fn data/TestSet/ -sl TestSet -t 32 > TestSet.log 2> TestSet.err
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So I know this is not the GitHub repository for the pan-genome-visualization package but I am super lost regarding how to make the visualization work.
What exactly are the arguments to be used for…
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is it possible to use query_pan_genome with a percentage, just as roary? For example, when comparing two groups, be able to set thresholds like "max 30% present in group 1, min 70% present in group 2"…
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Hi
I have able to successfully get the pan-genome, core genome and accessory genome from our isolates. What I am also interested is getting unique genes from each isolates. I am wondering if there …
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Hello everyone,
I am trying to run pan-genome analysis on 32 AOA species using the full genebanks I obtained from the NCBI and this code
./panX.py -fn data/genebanks -sl pratice -t 6
Howeve…