Issue with Pangenome Analysis of S. thermophilus Isolates

I am writing to bring to your attention an issue I encountered while conducting pangenome analysis using Roary on Galaxy.

Specifically, I have been attempting to analyze the pangenome of 15 S. thermophilus isolates, for which annotation was performed using Prokka. Despite following the standard procedures and ensuring the data inputs are accurate, I have consistently encountered a problem where no results are generated for the genes of interest. Upon careful examination, it appears that the data pertaining to the genes of interest consistently show zero counts. what is wrong witht that?

Hi @deniz_KIRAZ
What do you mean by “zero counts”? Do you mean that genes of interest are present in Roary output? If yes, can you check if the genes of interest were annotated by Prokka in each sample? If the genes were annotated only in some samples, make sure you adjust “percentage of isolates a gene must be in to be core”. The default value is very high, and for your set it means core genes must present in all samples. If the genes of interest are not very conservative, consider reducing minimum percentage identity for blastp.

Hope that helps.
Kind regards,

Thank you for your response to my query. I appreciate your assistance. I successfully performed annotation using the Kbase web-based online system. Despite adjusting the default values as you suggested and even lowering them further, I still couldn’t conduct the pangenome analysis for the isolates at hand.