search

gtonkinhill / panaroo

An updated pipeline for pangenome investigation
MIT License
269 stars 34 forks source link

Low number of genes as output #309

Closed AzizHN closed 1 month ago

AzizHN commented 1 month ago

I run a panaroo test using 2 gff files, containing 1758 and 1553 genes, but in summary resulted from panaroo (strict clean-mode) I have this: Core genes (99% <= strains <= 100%) 26 Soft core genes (95% <= strains < 99%) 0 Shell genes (15% <= strains < 95%) 1 Cloud genes (0% <= strains < 15%) 0 Total genes (0% <= strains <= 100%) 27

gtonkinhill commented 1 month ago

Hi,

It is usually best to run panaroo on at least 10 genomes when using the strict mode. I would try running it using the sensitive option if you are only interested in a couple of genomes.