Matchless comparison between Roary and Prokka: missing genes in "gene_presence_abscence.csv"

Question

[greed]

Hi there! I recently ran Roary for some bacterial strains using GFF annotations produced via Prokka. Then I examined the outputs and I noticed that some gene IDs that are present in the GFF annotation of Prokka, are actually missing in the "gene_presence_abscence.csv" produced by Roary. How's that possible? Thank you.

[andres.firrincieli]

What kind of genes are you missing? As far as I know Roary only works with protein coding genes

[greed]

In Prokka annotation, the ID is an "hypothetical protein"

[andres.firrincieli]

the ID is an "hypothetical protein"

That is the gene product name not the gene ID.

By the way, I had a similar issue with a different software (Anvi'o). It came out that truncated genes or genes spanning across multiple contigs were not included in the pan-genome analysis. I would manually check some of these genes and try to understand why they are missing in the pan-genome.

I'm sorry I couldn't be more helpful

[greed]

Thank you, you've been helpful.