text: user939: I recently installed Ubuntu 16.04 (because I was still using 12.04). But it seems my bedtools scripts don't work properly anymore. I can't figure out how to use the new bedtools for my old ways. What I want to do is get the number of reads from a bam file, per interval from a bed file. It was very simple with my old version of Ubuntu and bedtools:
  bedtools coverage -abam file.bam -b All_peaks.bed > file.cov.txt
  
  But this doesn't seem to work anymore. I used to get small files as results (~3MB), but now huge files are created (~4GB) including read names??
  I am using bedtools v2.25 now.
  
  user77: The order of -a and -b switched at some point. You want:
  bedtools coverage -a All_peaks.bed -b file.bam > file.cov.txt
  
  For reference, this is the end of the help output in version 2.25:
  Default Output:  
       After each entry in A, reports: 
         1) The number of features in B that overlapped the A interval.
         2) The number of bases in A that had non-zero coverage.
         3) The length of the entry in A.
         4) The fraction of bases in A that had non-zero coverage.
  
  And this is the equivalent output from version 2.19:
  Default Output:  
       After each entry in B, reports: 
         1) The number of features in A that overlapped the B interval.
         2) The number of bases in B that had non-zero coverage.
         3) The length of the entry in B.
         4) The fraction of bases in B that had non-zero coverage.
  
  Update: The change in behavior happened in version 2.24:
  
  We have changed the behavior of the coverage tool such that it is consistent with the other tools. Specifically, coverage is now
    computed for the intervals in the A file based on the overlaps with the B file, rather than vice versa.
  
  
original_text: 939: <p>I recently installed Ubuntu 16.04 (because I was still using 12.04). But it seems my bedtools scripts don't work properly anymore. I can't figure out how to use the new bedtools for my old ways. What I want to do is get the number of reads from a bam file, per interval from a bed file. It was very simple with my old version of Ubuntu and bedtools:</p>
  
  <pre><code>bedtools coverage -abam file.bam -b All_peaks.bed &gt; file.cov.txt
  </code></pre>
  
  <p>But this doesn't seem to work anymore. I used to get small files as results (~3MB), but now huge files are created (~4GB) including read names??</p>
  
  <p>I am using bedtools v2.25 now.</p>
   77: <p>The order of <code>-a</code> and <code>-b</code> switched at some point. You want:</p>
  
  <pre><code>bedtools coverage -a All_peaks.bed -b file.bam &gt; file.cov.txt
  </code></pre>
  
  <p>For reference, this is the end of the help output in version 2.25:</p>
  
  <pre><code>Default Output:  
       After each entry in A, reports: 
         1) The number of features in B that overlapped the A interval.
         2) The number of bases in A that had non-zero coverage.
         3) The length of the entry in A.
         4) The fraction of bases in A that had non-zero coverage.
  </code></pre>
  
  <p>And this is the equivalent output from version 2.19:</p>
  
  <pre><code>Default Output:  
       After each entry in B, reports: 
         1) The number of features in A that overlapped the B interval.
         2) The number of bases in B that had non-zero coverage.
         3) The length of the entry in B.
         4) The fraction of bases in B that had non-zero coverage.
  </code></pre>
  
  <p><strong>Update</strong>: The change in behavior happened in version 2.24:</p>
  
  <blockquote>
    <p>We have changed the behavior of the coverage tool such that it is consistent with the other tools. Specifically, coverage is now
    computed for the intervals in the A file based on the overlaps with the B file, rather than vice versa.</p>
  </blockquote>
  