<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>

CC BY-SA 4.0
2022-05-11T02:10:12.993Z
consider calling peaks with Genrich which will handle you replicates quite nicely.
malcook
CC BY-SA 4.0
2022-05-11T08:48:31.767Z
although I haven't used it but will give it try
kcm
<bed><peak-calling>
chip seq biological replicate merge after peak-calling
# 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

Peak calling
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
 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  

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## 0 answers

