Answers.Body: <p>This sort of procedure is done in tool papers to benchmark results compared to different aligners/mappers. See the salmon or kallisto papers for examples. Using the intersect of DE results from different mappers will end up yielding somewhat conservative results, not unlike using different differential expression packages and taking the intersect of their outputs. In practice you could just take a more conservative p-value cut-off and save the hassle of using multiple tools, the results would end up being similar.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-12T11:05:16.610Z
Answers.Text: Yes, I have read in tutorials that the best approach would be to find the intersection of DEGs produced by different algorithms (deseq2, limmavoom, edger) and that s the reason why I wondered if I should the same with the aligner as well.. Thank you for your answer!
Answers.UserDisplayName: marilu
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-12T07:35:17.437Z
Answers.LastActivityDate: 2020-11-12T07:35:17.437Z
Answers.UserDisplayName: Devon Ryan
Body: <p>I would like to ask if someone uses two different aligners to produce count matrices and then run the same alogrithm for DEG analysis, would it make sense to find the intersection of the DEGs in order to conclude to the &quot;real&quot; DEGS?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-11-11T16:17:02.587Z
Comments.Text: Thank you so much for your feedback!Yes that particular problem I am trying to solve..!
Comments.UserDisplayName: marilu
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-11-11T16:42:27.157Z
Comments.Text: No, I am just trying to understand which algorithm to trust and which approach would give the most reliable results.. I am not trying to tweak results..
Comments.UserDisplayName: marilu
Tags: <rna-seq>
Title: two aligners combined results
ThreadText: # two aligners combined results
  
  (Asked by: username_0 on 2020-11-11)
  
  I would like to ask if someone uses two different aligners to produce count matrices and then run the same alogrithm for DEG analysis, would it make sense to find the intersection of the DEGs in order to conclude to the "real" DEGS?
  
  **Tags:** rna-seq
  
  > **Comments:**
  > **username_0**: Thank you so much for your feedback!Yes that particular problem I am trying to solve..!  
  > **username_0**: No, I am just trying to understand which algorithm to trust and which approach would give the most reliable results.. I am not trying to tweak results..  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2020-11-12. Score: 1
  
  This sort of procedure is done in tool papers to benchmark results compared to different aligners/mappers. See the salmon or kallisto papers for examples. Using the intersect of DE results from different mappers will end up yielding somewhat conservative results, not unlike using different differential expression packages and taking the intersect of their outputs. In practice you could just take a more conservative p-value cut-off and save the hassle of using multiple tools, the results would end up being similar.
  
  > **Comments:**
  > **username_0**: Yes, I have read in tutorials that the best approach would be to find the intersection of DEGs produced by different algorithms (deseq2, limmavoom, edger) and that s the reason why I wondered if I should the same with the aligner as well.. Thank you for your answer!  
  
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