Answers.Body: <ol>
  <li>Convert each of your Excel spreadsheets to tab-delimited text files (<a href="https://www.howtogeek.com/79991/convert-an-excel-spreadsheet-to-a-tab-delimited-text-file/" rel="nofollow noreferrer">how-to</a>).</li>
  <li><a href="https://cygwin.com/install.html" rel="nofollow noreferrer">Install and run Cygwin</a>, if using Windows. If you are using OS X, open up the Terminal app.</li>
  <li><a href="https://bedops.readthedocs.io/en/latest/content/installation.html" rel="nofollow noreferrer">Install the BEDOPS toolkit</a> to get sorting and set operation tools (if you're not averse to using them).</li>
  <li><p>Strip out the Microsoft line endings, strip the header, and sort each of the <em>N</em> files:</p>
  
  <pre><code>$ tr -d '\r' &lt; fileN.tsv | tail -n+2 - | sort-bed - &gt; fileN.bed
  </code></pre></li>
  <li><p>Merge the files:</p>
  
  <pre><code>$ bedops --merge file1.bed file2.bed ... fileN.bed &gt; answer.bed
  </code></pre></li>
  </ol>
  
  <p>The file <code>answer.bed</code> will contain all merged regions from files <code>file1.bed</code> through <code>fileN.bed</code>. Merging will be done on intervals for each unique chromosome name.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-04T20:47:47.863Z
Answers.Text: Thanks that worked
Answers.UserDisplayName: Mariam
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-03T07:33:53.447Z
Answers.LastActivityDate: 2020-04-03T07:33:53.447Z
Answers.UserDisplayName: Alex Reynolds
Answers.Body: <p>In my opinion, the easiest way to merge bed files is to use <code>bedtools merge</code>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-04T15:17:45.307Z
Answers.LastActivityDate: 2020-04-04T15:17:45.307Z
Answers.UserDisplayName: Phoenix Mu
Answers.Body: <p>To merge multiple BED files into one, you need to do the following:</p>
  <ul>
  <li>concatenate them all (<code>bedtools merge</code> only accepts one input BED)</li>
  <li>sort the concatenated BED</li>
  <li>merge the sorted BED with <a href="https://bedtools.readthedocs.io/en/latest/content/tools/merge.html" rel="nofollow noreferrer"><code>bedtools merge</code></a></li>
  </ul>
  <p>Here is a simple pipeline to do this</p>
  <pre><code>cat a.bed b.bed | sort -k 1,1 -k2,2n | bedtools merge &gt; merged.bed
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-07-05T02:27:24.277Z
Answers.LastActivityDate: 2024-07-05T02:27:24.277Z
Answers.UserDisplayName: Michael Hall
Body: <p>I am trying to merge two bed files (more in future) to one. my bed files are something like : 
  <a href="https://i.sstatic.net/dcAAi.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/dcAAi.png" alt="result of macs pea calling"></a>.</p>
  
  <p>I need to merge them in a way to have the shared chromosome location. </p>
  
  <p>Is there a way to do that ?</p>
  
Tags: <phylogenetics><samtools><sequence-analysis><bedtools><macs2>
Title: merging two/or more bed file into one bed file
ThreadText: # merging two/or more bed file into one bed file
  
  (Asked by: username_0 on 2020-04-03)
  
  I am trying to merge two bed files (more in future) to one. my bed files are something like :
  [![result of macs pea calling](https://i.sstatic.net/dcAAi.png)](https://i.sstatic.net/dcAAi.png).
  
  I need to merge them in a way to have the shared chromosome location.
  
  Is there a way to do that ?
  
  **Tags:** phylogenetics, samtools, sequence-analysis, bedtools, macs2
  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_1 on 2020-04-03. Score: 3
  
  1. Convert each of your Excel spreadsheets to tab-delimited text files ([how-to](https://www.howtogeek.com/79991/convert-an-excel-spreadsheet-to-a-tab-delimited-text-file/)).
  2. [Install and run Cygwin](https://cygwin.com/install.html), if using Windows. If you are using OS X, open up the Terminal app.
  3. [Install the BEDOPS toolkit](https://bedops.readthedocs.io/en/latest/content/installation.html) to get sorting and set operation tools (if you're not averse to using them).
  4. Strip out the Microsoft line endings, strip the header, and sort each of the *N* files:
  
     ```
     $ tr -d '\r' < fileN.tsv | tail -n+2 - | sort-bed - > fileN.bed
  
     ```
  5. Merge the files:
  
     ```
     $ bedops --merge file1.bed file2.bed ... fileN.bed > answer.bed
  
     ```
  
  The file `answer.bed` will contain all merged regions from files `file1.bed` through `fileN.bed`. Merging will be done on intervals for each unique chromosome name.
  
  > **Comments:**
  > **username_0**: Thanks that worked  
  
  ---
  
  ### Answer by username_2 on 2020-04-04. Score: 2
  
  In my opinion, the easiest way to merge bed files is to use `bedtools merge`.
  
  
  ---
  
  ### Answer by username_3 on 2024-07-05. Score: 0
  
  To merge multiple BED files into one, you need to do the following:
  
  * concatenate them all (`bedtools merge` only accepts one input BED)
  * sort the concatenated BED
  * merge the sorted BED with [`bedtools merge`](https://bedtools.readthedocs.io/en/latest/content/tools/merge.html)
  
  Here is a simple pipeline to do this
  
  ```
  cat a.bed b.bed | sort -k 1,1 -k2,2n | bedtools merge > merged.bed
  
  ```
  
  
  ---
  
  