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AdmiralenOla / Scoary

Pan-genome wide association studies
GNU General Public License v3.0
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Splitting paralogs influence to Scoary? #79

Closed nbawe closed 4 years ago

nbawe commented 4 years ago

@AdmiralenOla does not splitting paralogs (-s in roary) affect Scoary results?

AdmiralenOla commented 4 years ago

Hi, @nbawe. Scoary actually doesn't care what parameters you used in Roary at all. It simply accepts the input files as "the truth".

If Roary split paralogs into multiple genes in your gene presence/absence file, then Scoary will never know that these genes are paralogs. It will treat them as two distinct units.

On a related note, I know some people have problems with Roary being overly enthusiastic about splitting genes that from an evolutionary point of view are the same. If you have problems with this I suggest using the pan-genome program Panaroo instead. It is less prone to split genes that have identical genomic neighborhood for example. It is available at Gerry Tonkin-Hill's github: https://github.com/gtonkinhill/panaroo

AdmiralenOla commented 4 years ago

Since it is not really an issue I'll be closing this