Answers.Body: <p>Looking at this again, I have now worked out (and should probably have noticed previously) that the 'source Gene ID' field from the 'gene_presence_absence.csv' file originates from the ID field of the .gff file for the sequence in question.</p>
  <p>You can therefore easily tie the results from the 'gene_presence_absence.csv' file back to the annotation from the sequence in question, and therefore to the location of the nucleotide sequence for the gene in question.</p>
  <p>So for instance, if you take a 'source Gene ID' from the gene_presence_absence file - say <code>GEICCBEJ_00950</code> - and use it in a grep command referencing the genome from which it came, <code>grep &quot;GEICCBEJ_00950&quot; my_annotation_file.gff</code>, then you should see the line from the annotation corresponding to this sequence.</p>
  <p>The 'source Gene ID' is also referenced in the pan_genome_reference.fa output from ROARY, which gives &quot;single representative nucleotide sequence from each of the clusters in the pan genome (core and accessory)&quot;.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-06-28T19:36:44.013Z
Answers.LastActivityDate: 2021-06-28T19:36:44.013Z
Answers.UserDisplayName: Mark
Body: <p>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 <a href="https://sanger-pathogens.github.io/Roary/" rel="nofollow noreferrer">Roary web page</a> states that this is:</p>
  <ol start="15">
  <li>Presence and absence of genes in each sample, with the corresponding source Gene ID.</li>
  </ol>
  <p>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 <code>Grep</code> in the directory containing my .gff files I get no matches, so I am assuming it is generated by Roary...?</p>
  <p>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?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-06-23T23:50:19.877Z
Comments.Text: Did you end up getting an answer to this question? I have the same question.
Comments.UserDisplayName: Sharb
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-06-28T19:37:46.000Z
Comments.Text: @Sharb - I think i can now answer this question.  I have added an answer.  Let me know if you fee it needs any clarification?
Comments.UserDisplayName: Mark
Tags: <genome><genomics><bacteria>
Title: What is the origin of the 'source Gene ID' references given in the 'gene_presence_absence.csv' output of Roary?
ThreadText: # What is the origin of the 'source Gene ID' references given in the 'gene_presence_absence.csv' output of Roary?
  
  (Asked by: username_0 on 2020-07-03)
  
  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](https://sanger-pathogens.github.io/Roary/) states that this is:
  
  15. 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?
  
  **Tags:** genome, genomics, bacteria
  
  > **Comments:**
  > **username_1**: Did you end up getting an answer to this question? I have the same question.  
  > **username_0**: @username_1 - I think i can now answer this question.  I have added an answer.  Let me know if you fee it needs any clarification?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2021-06-28. Score: 1 | Accepted answer
  
  Looking at this again, I have now worked out (and should probably have noticed previously) that the 'source Gene ID' field from the 'gene\_presence\_absence.csv' file originates from the ID field of the .gff file for the sequence in question.
  
  You can therefore easily tie the results from the 'gene\_presence\_absence.csv' file back to the annotation from the sequence in question, and therefore to the location of the nucleotide sequence for the gene in question.
  
  So for instance, if you take a 'source Gene ID' from the gene\_presence\_absence file - say `GEICCBEJ_00950` - and use it in a grep command referencing the genome from which it came, `grep "GEICCBEJ_00950" my_annotation_file.gff`, then you should see the line from the annotation corresponding to this sequence.
  
  The 'source Gene ID' is also referenced in the pan\_genome\_reference.fa output from ROARY, which gives "single representative nucleotide sequence from each of the clusters in the pan genome (core and accessory)".
  
  
  ---
  
  