text: user4836: I have two files of genomic coordinates. I am trying to output only the overlapping region of fileA if it intersects with fileB. Not the original fileA coordinates.
  fileA
  chr1 25 50
  chr1 75 200
  
  fileB
  chr1 10 60
  chr1 80 90
  
  desired output
  chr1 25 50
  chr1 80 90
  
  
  user96: bedtools is my go-to program for operations on genomic intervals. In particular, the bedtools intersect operation is what you're looking for here.
  $ cat fileA
  chr1    25      50
  chr1    75      200
  $ cat fileB
  chr1    10      60
  chr1    80      90
  $ bedtools intersect -a fileA -b fileB                                                           
  chr1    25      50
  chr1    80      90
  
  Make sure that the values are separated by tabs rather than spaces, or bedtools will have trouble reading the files.
  
original_text: 4836: <p>I have two files of genomic coordinates. I am trying to output only the overlapping region of fileA if it intersects with fileB. Not the original fileA coordinates.</p>
  
  <p>fileA</p>
  
  <pre><code>chr1 25 50
  chr1 75 200
  </code></pre>
  
  <p>fileB</p>
  
  <pre><code>chr1 10 60
  chr1 80 90
  </code></pre>
  
  <p>desired output</p>
  
  <pre><code>chr1 25 50
  chr1 80 90
  </code></pre>
   96: <p><a href="https://bedtools.readthedocs.io/en/latest/index.html" rel="nofollow noreferrer">bedtools</a> is my go-to program for operations on genomic intervals. In particular, the <a href="https://bedtools.readthedocs.io/en/latest/index.html" rel="nofollow noreferrer">bedtools intersect</a> operation is what you're looking for here.</p>
  
  <pre><code>$ cat fileA
  chr1    25      50
  chr1    75      200
  $ cat fileB
  chr1    10      60
  chr1    80      90
  $ bedtools intersect -a fileA -b fileB                                                           
  chr1    25      50
  chr1    80      90
  </code></pre>
  
  <p>Make sure that the values are separated by tabs rather than spaces, or bedtools will have trouble reading the files.</p>
  