Answers.Body: <p>I am not an expert on recent packages but I would suggest using <a href="http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/" rel="nofollow noreferrer">Matrix eQTL</a> for purposes of the statistical analysis.</p>
  <p>As mentioned in the comments I think that it is worth testing <em>all</em> transcripts for eQTL associations. This will additionally give some idea of the false discovery rate. It is possible that testing &quot;candidate gene&quot; differentially expressed genes will lead to a lot of false positives relative to the background level of associations.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-09-29T16:30:24.487Z
Answers.LastActivityDate: 2021-09-29T16:30:24.487Z
Answers.UserDisplayName: Maximilian Press
Body: <p>I want to do a GWAS analysis using the differentially expressed genes that I got from a differential analysis. The purpose is the identification of biomarkers.</p>
  <p>It's my first time using GWAS, can you please suggest to me a pipeline to use?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-09-27T16:54:36.680Z
Comments.Text: If you are looking for biomarkers, why not look at all genes? There will be a lot more information there.
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-09-28T12:34:11.283Z
Comments.Text: ok thank u,  so we have to use all genes as phenotypes.
  it's my first time using GWAS, can you suggest me a pipeline to use.
Comments.UserDisplayName: Zahrae
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-09-29T15:50:23.883Z
Comments.Text: @MaximilianPress
Comments.UserDisplayName: Zahrae
Tags: <gwas>
Title: Gwas analysis studies using the result of differential analysis
ThreadText: # Gwas analysis studies using the result of differential analysis
  
  (Asked by: username_0 on 2021-09-26)
  
  I want to do a GWAS analysis using the differentially expressed genes that I got from a differential analysis. The purpose is the identification of biomarkers.
  
  It's my first time using GWAS, can you please suggest to me a pipeline to use?
  
  **Tags:** gwas
  
  > **Comments:**
  > **username_1**: If you are looking for biomarkers, why not look at all genes? There will be a lot more information there.  
  > **username_0**: ok thank u,  so we have to use all genes as phenotypes. it's my first time using GWAS, can you suggest me a pipeline to use.  
  > **username_0**: @username_1  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2021-09-29. Score: 0 | Accepted answer
  
  I am not an expert on recent packages but I would suggest using [Matrix eQTL](http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/) for purposes of the statistical analysis.
  
  As mentioned in the comments I think that it is worth testing *all* transcripts for eQTL associations. This will additionally give some idea of the false discovery rate. It is possible that testing "candidate gene" differentially expressed genes will lead to a lot of false positives relative to the background level of associations.
  
  
  ---
  
  