Using reference genome for GSEA for different strains of the same bacterial species

Question

[Texx]

I have several strains of the same bacterial species for which there exists a high-quality and annotated reference genome, but not separately for every single strain.

Is it acceptable to perform the differential expression analysis and particularly GSEA (gene-set enrichment analysis) using tools like ClusterProfiler using the available reference genome for each of the different strains, even if the strains are slightly different (though still technically the same species and even subspecies)?

Answer 1

[Istvan Albert]

When it comes to GSEA and enrichment studies ... I wouldn't worry about small differences.

The handwaving within of gene enrichment analysis is rampant ... the choice of background and methodology, data builds, is far more impactful and still practically ignored