Roary

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While using the command "query_pan_genome -a intersection *.gff", I am getting the error: " Error: Cant access file Roary_output/vA2CRQZLas (where 'Roary_output' are self made folders and 'vA2CRQZLas' is the random...

Ujjwal-Madaan

MSG: '' is not a valid frame

1

I'm pulling gff files in from IMG genomes. IMG has the data parsed into gff and fna files already along with some other files. I've mergred the gff and fna...

Bleed242

Unique genes issue

3

Hi there, I'm running a pangenome analyisis on 20 bacterial strains using roary version 3.13, on a server running CentOS 7. I want to get the unique genes present in...

Sirbius

Hi I use this parameters，but I find 100 indentity sequence are different groups why? ``` roary $gff --mafft -r -p $thread -i 95 -cd 100 -f $roary/roary_95_out ``` 

zckoo007

Cant open file: _clustered.clstr

3

Hello, running Roary/1.13.0 we have a problem running roary, it stops with the following error message: ``` Iteratively run cd-hit Cant open file: _clustered.clstrParallel all against all blast ``` after...

EricDeveaud

SyntaxError: invalid syntax

1

Hi all, I am running roary_plots.py, I've downloaded the script of "roary_plots.py " and trying to run the next code: roary_plots.py mytree.nwk gene_presence_absence.csv I got the following: SyntaxError: invalid syntax...

TC-2021

Error: Cant access file -­a

2

Hi, I'd like to extract the core genes for each sample with the following command `query_pan_genome ­a intersection ­g clustered_proteins *.gff` However, I got the error - _Error: Cant access...

ZhangDengwei

Hello, I only have a quick question. If this tree is based on the binary presence and absence of accessory genes, what does the distance in the tree means? I...

EllistonV

Hi, Some of My Output Data is named as "group_xxx" without any annotation assigned. Is there some way to find the sequences associated to that group? Any help would be...

ThomasPuttingGenomesTogether

Is there any way to compare core genes from two different pan genome results on Roary?

1

Hello, I was wondering if there is a way to compare core genes from two different groups A and B (n=100 for each group) which are all same species (E....

djung0928