Answers.Body: <p>If you want to find the intersection between ALL your bedfiles, you can try <code>multiIntersectBed</code> (available since bedtools 2.14.3).</p>
  
  <p>It should work like this :</p>
  
  <pre><code>multiIntersectBed -i SRR2920506.filtered.bed SRR2920531.filtered.bed SRR2920466.filtered.bed SRR2920478.filtered.bed SRR2920507.filtered.bed SRR2920532.filtered.bed  &gt; answer.bed
  </code></pre>
  
  <p>To sort your bedfiles by chromosome then by start :</p>
  
  <pre><code>sort -k 1,1 -k2,2n myfile.bed
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-21T16:27:54.093Z
Answers.Text: ERROR: input file: (SRR2920466.filtered.bed) is not sorted by chrom then start. this came as i tried with multiIntersectBed
Answers.UserDisplayName: kcm
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-21T16:36:34.090Z
Answers.Text: Yep this is described as the second line of the usage. I just updated the answer
Answers.UserDisplayName: Paul Endymion
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-21T16:26:59.547Z
Answers.LastActivityDate: 2019-11-21T16:33:25.133Z
Answers.LastEditDate: 2019-11-21T16:33:25.133Z
Answers.UserDisplayName: Paul Endymion
Body: <p>I have 7 biological replicate of a normal sample after peak-calling I converted it into bed files and now I want to find what are the common region between those .</p>
  
  <p>So i tried with bedtool intersect </p>
  
  <pre><code>my command is this 
  bedtools intersect -a SRR2920506.filtered.bed -b SRR2920531.filtered.bed SRR2920466.filtered.bed SRR2920478.filtered.bed SRR2920507.filtered.bed SRR2920532.filtered.bed  &gt; answer.bed
  </code></pre>
  
  <p>it says " the intersect tool can detect overlaps between a single -a file and multiple -b files (instead of just one previously). One simply provides multiple -b files on the command line."</p>
  
  <p>My doubt is the file that goes to "a" argument is not query which i have to detect overlaps against "b" files as these are all biological replicate. Am i doing the right way?</p>
  
  <p>Secondly I tried with <code>bedops</code> but the number of overlaps which is reported is really low when i compare the result which i get from bedtools intersect function.</p>
  
  <p>Any suggestion or help regarding how to intersect multiple would be really appreciated </p>
  
Tags: <bedtools>
Title: bedtool intersect multiple bed files
ThreadText: # bedtool intersect multiple bed files
  
  (Asked by: username_0 on 2019-11-21)
  
  I have 7 biological replicate of a normal sample after peak-calling I converted it into bed files and now I want to find what are the common region between those .
  
  So i tried with bedtool intersect
  
  ```
  my command is this 
  bedtools intersect -a SRR2920506.filtered.bed -b SRR2920531.filtered.bed SRR2920466.filtered.bed SRR2920478.filtered.bed SRR2920507.filtered.bed SRR2920532.filtered.bed  > answer.bed
  
  ```
  
  it says " the intersect tool can detect overlaps between a single -a file and multiple -b files (instead of just one previously). One simply provides multiple -b files on the command line."
  
  My doubt is the file that goes to "a" argument is not query which i have to detect overlaps against "b" files as these are all biological replicate. Am i doing the right way?
  
  Secondly I tried with `bedops` but the number of overlaps which is reported is really low when i compare the result which i get from bedtools intersect function.
  
  Any suggestion or help regarding how to intersect multiple would be really appreciated
  
  **Tags:** bedtools
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-11-21. Score: 5 | Accepted answer
  
  If you want to find the intersection between ALL your bedfiles, you can try `multiIntersectBed` (available since bedtools 2.14.3).
  
  It should work like this :
  
  ```
  multiIntersectBed -i SRR2920506.filtered.bed SRR2920531.filtered.bed SRR2920466.filtered.bed SRR2920478.filtered.bed SRR2920507.filtered.bed SRR2920532.filtered.bed  > answer.bed
  
  ```
  
  To sort your bedfiles by chromosome then by start :
  
  ```
  sort -k 1,1 -k2,2n myfile.bed
  
  ```
  
  > **Comments:**
  > **username_0**: ERROR: input file: (SRR2920466.filtered.bed) is not sorted by chrom then start. this came as i tried with multiIntersectBed  
  > **username_1**: Yep this is described as the second line of the usage. I just updated the answer  
  
  ---
  
  