Roary

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I have a question about the first core step: cluster fasta by ch-hit iteratively which is also the key step to reducing the number of proteins. Why we need to...

bucongfan

Error: Cant access the groups file: clustered_proteins

2

$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 Perform set operations on the pan genome to see the gene differences...

ryu1013

I have a set of 100 bacterial genomes. I annotated them with Prokka and performed pangenome analysis with Roary. Roary outputs the core gene alignment file which I then used...

chahatupreti

Hi, when I open the file "gene_presence_absence.csv" in LinerOffice Calc, it takes wrong indentation and replacing empty cells in "" and adding "" with every word in each line.

sekhwal

I ask you to help me, as I need to identify the genetic sequences that characterize the groups in the roary pangenome tool. It generates a file with present and...

Deblusantos

Issue with "Error: Cant access the groups file: clustered_proteins"

1

I am sorry about this question, because I know somebody asked this issue before, and the answer was the checking the directory. But, I can not run the "query_pan_genome" properly....

wayne1215

cann't install roary 3.13 with mamba/conda

1

I tried to install roary with mamba but got: ``` package roary-3.13.0-pl526h516909a_0 requires perl-text-csv, but none of the providers can be installed ``` If I use conda, it will show:...

dawnmy

The singularity image pulled from docker://sangerpathogens/roary does not accept input gff files

2

Since conda failed to install roary, I switched to use singularity. I pulled the image with ```shell singularity pull roary.sif docker://sangerpathogens/roary ``` But when I run the command: ```shell singularity...

dawnmy

Strange Ouput

2

Hi! I'm trying to build a pangenome using Roary. However, I got some strange outputs and some warning. **The code I ran:** **(Roary) login-2:roary$ roary -p 128 *.gff -i 90...

ShuyiF

Hi, I ran the suggested code for a core alignment (roary -e --mafft -p 8 *.gff) and the output alignment file has a combination of lower and upper case sequences...

samuelmontgomery