I am learning to use Roary for preparing a pan genome for some lactobacillus strains. In the 'gene_presence_absence.csv' output of Roary (which I view in excel), a 'source Gene ID' is given for each of the strains included in the analysis. The Roary web page states that this is:
- Presence and absence of genes in each sample, with the corresponding source Gene ID.
Is this 'source Gene ID' generated by Roary, or does it relate back directly to the .gff files I used as input? If I take one of these 'source Gene ID' references and
Grep in the directory containing my .gff files I get no matches, so I am assuming it is generated by Roary...?
I had hoped that this reference would link back directly to the gene within the annotation file, but that seems not to be the case? Should/can I use this reference for anything?