Body: <p>I have 3 biological replicates for KO condition. What I have done so far</p>
  <ol>
  <li>Peak calling</li>
  <li>The removed blacklisted region</li>
  </ol>
  <p>Now Im bit confused about the peak merging stage. Here Im trying to use the bedops tool.</p>
  <p>So what is the best option in my case when I want to make a combined set of peaks that is present in all the three replicates what option do i have to use?</p>
  <p>Which option to use from <a href="https://bedops.readthedocs.io/en/latest/content/reference/set-operations.html" rel="nofollow noreferrer">bedops</a></p>
  <pre><code> Everything (-u, –everything) or `Merge (-m, –merge)`
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-05-11T02:10:12.993Z
Comments.Text: consider calling peaks with Genrich which will handle you replicates quite nicely.
Comments.UserDisplayName: malcook
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-05-11T08:48:31.767Z
Comments.Text: although I haven't used it but will give it try
Comments.UserDisplayName: kcm
Tags: <bed><peak-calling>
Title: chip seq biological replicate merge after peak-calling
ThreadText: # chip seq biological replicate merge after peak-calling
  
  (Asked by: username_0 on 2022-05-10)
  
  I have 3 biological replicates for KO condition. What I have done so far
  
  1. Peak calling
  2. The removed blacklisted region
  
  Now Im bit confused about the peak merging stage. Here Im trying to use the bedops tool.
  
  So what is the best option in my case when I want to make a combined set of peaks that is present in all the three replicates what option do i have to use?
  
  Which option to use from [bedops](https://bedops.readthedocs.io/en/latest/content/reference/set-operations.html)
  
  ```
   Everything (-u, –everything) or `Merge (-m, –merge)`
  
  ```
  
  **Tags:** bed, peak-calling
  
  > **Comments:**
  > **username_1**: consider calling peaks with Genrich which will handle you replicates quite nicely.  
  > **username_0**: although I haven't used it but will give it try  
  
  ---
  
  ## 0 answers
  
  