Answers.Body: <p>Did you try query_pan_genome?</p>
  <p>Ref. <a href="https://sanger-pathogens.github.io/Roary/" rel="nofollow noreferrer">https://sanger-pathogens.github.io/Roary/</a></p>
  
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Answers.UserDisplayName: Joe Ba
Body: <p>I performed a ROARY from 100 genome. I got several file including gene_presence_absence.csv  from the results. I want to know how many unique gene(unshared gene, based on blast homology, same gene (duplicate gene) may be unique if no homology is there between them) from presence absence csv file or other file. Kindly suggest me how to calculate total number of unique gene for each genome which is only present in one genome</p>
  
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Comments.Text: How do you define "unique genes"? Unique to what? You mean genetic sequences that code for protein which are only present once in a given genome? Do you mean unique to that species? Unique how? In terms of sequence? In terms of function? How much similarity do you allow? What species are you working with? Please [edit] your question and explain what you need and also what kind of data you have more clearly.
Comments.UserDisplayName: terdon
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Comments.CreationDate: 2023-03-15T13:32:46.103Z
Comments.Text: Thank you for the reply, based on presence absence  gene data file, only gene found in one genome but absent in other genome is considered as unique gene, ROARY use use presence absence data based on blast homology of protein within selected protein so, at end I want to get only unique gene from the table generated by PROKKA in gene presence absence csv file.
Comments.UserDisplayName: Umar
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Comments.CreationDate: 2023-03-15T13:43:20.407Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
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Comments.CreationDate: 2023-03-15T14:57:11.163Z
Comments.Text: Once I did ROARY, I got several files, right, there will be some shared gene, core gene , and unique gene, right, I want to know how many unshared gene (unique gene) are present in every genome.
Comments.UserDisplayName: Umar
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Comments.CreationDate: 2023-03-15T16:16:19.853Z
Comments.Text: Please [edit] your question and provide us with an example input file and the output you would expect.
Comments.UserDisplayName: terdon
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Comments.CreationDate: 2023-03-16T09:01:18.453Z
Comments.Text: I am trying to understand ROARY output results , sure I will do
Comments.UserDisplayName: Umar
Tags: <r><phylogeny><reference-genome>
Title: Calculating total number of Unique gene in every genome from ROARY pangenome output
ThreadText: # Calculating total number of Unique gene in every genome from ROARY pangenome output
  
  (Asked by: username_0 on 2023-03-15)
  
  I performed a ROARY from 100 genome. I got several file including gene\_presence\_absence.csv from the results. I want to know how many unique gene(unshared gene, based on blast homology, same gene (duplicate gene) may be unique if no homology is there between them) from presence absence csv file or other file. Kindly suggest me how to calculate total number of unique gene for each genome which is only present in one genome
  
  **Tags:** r, phylogeny, reference-genome
  
  > **Comments:**
  > **username_1**: How do you define "unique genes"? Unique to what? You mean genetic sequences that code for protein which are only present once in a given genome? Do you mean unique to that species? Unique how? In terms of sequence? In terms of function? How much similarity do you allow? What species are you working with? Please [edit] your question and explain what you need and also what kind of data you have more clearly.  
  > **username_0**: Thank you for the reply, based on presence absence  gene data file, only gene found in one genome but absent in other genome is considered as unique gene, ROARY use use presence absence data based on blast homology of protein within selected protein so, at end I want to get only unique gene from the table generated by PROKKA in gene presence absence csv file.  
  > **username_2**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  > **username_0**: Once I did ROARY, I got several files, right, there will be some shared gene, core gene , and unique gene, right, I want to know how many unshared gene (unique gene) are present in every genome.  
  > **username_1**: Please [edit] your question and provide us with an example input file and the output you would expect.  
  > **username_0**: I am trying to understand ROARY output results , sure I will do  
  
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  ## 1 answers
  
  ### Answer by username_3 on 2023-09-26. Score: 0
  
  Did you try query\_pan\_genome?
  
  Ref. <https://sanger-pathogens.github.io/Roary/>
  
  > **Comments:**
  > **username_2**: Your answer could be improved with additional supporting information. Please [edit] to add further details, such as citations or documentation, so that others can confirm that your answer is correct. You can find more information on how to write good answers [in the help center](/help/how-to-answer).  
  
  ---
  
  