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sanger-pathogens / Roary

Rapid large-scale prokaryote pan genome analysis
http://sanger-pathogens.github.io/Roary
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Gene present in Prokka but absent in Roary #548

Open nikolomics opened 2 years ago

nikolomics commented 2 years ago

Hello all,

I have annotated a number of genomes with Prokka which they contain a gene of interest in their annotated files. However after Roary analysis (-i 80 and -cd 90) the gene is not present in the pangenome.fa. A BLAST analysis was performed to validate the absence of the gene. I am running Roary with -s and lower -cd values to see if that can change the outcome. What may have happened and how we can prevent it? Thanks!

djung0928 commented 2 years ago

Hello, Did you find the reason why this happens? I have experienced the same issue.

nikolomics commented 2 years ago

Hi,

I have performed further analysis and still the problem persists. I have run all different parameters (i and cd including -s) still same problem. The gene exists in all files from the annotation of Prokka but never results in full presence in roary files. Same goes for the related tool Panaroo. It will be great if we can manage to find a solution for this!

j-marin commented 1 year ago

Hi, I have exactly the same issue. Did anyone find the reason? Thanks! Julie