Answers.Body: <p>It's hard to say for sure without seeing the exact commands you used. However, Orthofinder identifies/defines single-copy orthologues as those genes present in a single copy in all species being compared in the analysis. If a BUSCO orthologue is present in more than one copy in one of the species being compared (could be multi-copy, could be fragmented etc.), then it won't be recovered as single copy by Orthofinder.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-05-03T07:44:28.020Z
Answers.Text: Thanks for your reply. I run `OrthoFinder` with default parameters. The BUSCO identified 1000+ complete single-copy genes but only 387 identified by OrthoFinder. I am trying to confirm whether BUSCO single-copy genes are true single-copy.
Answers.UserDisplayName: YP CHEN
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-04-29T12:37:56.593Z
Answers.LastActivityDate: 2021-04-29T12:37:56.593Z
Answers.UserDisplayName: frustrated_bioinformatician
Body: <p>Dear Orthofinder users and BUSCO users,</p>
  <p>Recently, I have assessed 30 genome annotataions <code>using BUSCO with lineage</code> dataset <code>ascomycota_odb10</code>, I got 1100+ complete and single-copy genes. But the <code>orthofinder</code>  only identified 300+ single-copy genes. Aneone else have encountered this similar problem?</p>
  <p>Thanks,</p>
  <p>Yanpeng</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-05-03T08:07:51.170Z
Comments.Text: I know what caused the difference. BUSCO uses more strict criterion to determine single-copy genes but manly of the result genes are identified as multicopy genes by OrthoFinder using less strict parameters.
Comments.UserDisplayName: YP CHEN
Tags: <orthologues><busco><orthofinder>
Title: Number of sing-copy genes identified by orthofinder is far less than BUSCO assessment?
ThreadText: # Number of sing-copy genes identified by orthofinder is far less than BUSCO assessment?
  
  (Asked by: username_0 on 2021-04-21)
  
  Dear Orthofinder users and BUSCO users,
  
  Recently, I have assessed 30 genome annotataions `using BUSCO with lineage` dataset `ascomycota_odb10`, I got 1100+ complete and single-copy genes. But the `orthofinder` only identified 300+ single-copy genes. Aneone else have encountered this similar problem?
  
  Thanks,
  
  Yanpeng
  
  **Tags:** orthologues, busco, orthofinder
  
  > **Comments:**
  > **username_0**: I know what caused the difference. BUSCO uses more strict criterion to determine single-copy genes but manly of the result genes are identified as multicopy genes by OrthoFinder using less strict parameters.  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2021-04-29. Score: 1
  
  It's hard to say for sure without seeing the exact commands you used. However, Orthofinder identifies/defines single-copy orthologues as those genes present in a single copy in all species being compared in the analysis. If a BUSCO orthologue is present in more than one copy in one of the species being compared (could be multi-copy, could be fragmented etc.), then it won't be recovered as single copy by Orthofinder.
  
  > **Comments:**
  > **username_0**: Thanks for your reply. I run `OrthoFinder` with default parameters. The BUSCO identified 1000+ complete single-copy genes but only 387 identified by OrthoFinder. I am trying to confirm whether BUSCO single-copy genes are true single-copy.  
  
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