text: user2257: I'd like to output a figure in +/-1kb around a center using computeMatrix as following command:  
  computeMatrix reference-point -S data.bw -R centers.bed -a 1000 -b 1000 -bs=10 -out newdata10.gz --referencePoint center
  
  The bed file is like:
  chr1 100 101
  
  If I change -bs=1, two outputs of the same input newdata10.gz are quite different. Which's correct with my commands? Maybe I don't understand the meaning of binsize option. 
  
  user77: Please don't send things like this to the deepTools mailing list and post them here.
  As I mentioned on the list, what you're likely being surprised by is that computeMatrix is not summing values, but taking the average in each bin. You can change this with the --averageTypeBins option (the default is mean, you presumably want sum).
  Update: For those wondering the cause of the confusion was due to not using --missingDataAsZero. In other words, including or not including NAs will lead to different results, since different numbers of values will be included.
  
original_text: 2257: <p>I'd like to output a figure in +/-1kb around a center using <a href="http://deeptools.readthedocs.io/en/latest/content/tools/computeMatrix.html" rel="nofollow noreferrer">computeMatrix</a> as following command:  </p>
  
  <pre><code>computeMatrix reference-point -S data.bw -R centers.bed -a 1000 -b 1000 -bs=10 -out newdata10.gz --referencePoint center
  </code></pre>
  
  <p>The bed file is like:</p>
  
  <pre><code>chr1 100 101
  </code></pre>
  
  <p>If I change <code>-bs=1</code>, two outputs of the same input newdata10.gz are quite different. Which's correct with my commands? Maybe I don't understand the meaning of binsize option. </p>
   77: <p>Please don't send things like this to the deepTools mailing list and post them here.</p>
  
  <p>As I mentioned on the list, what you're likely being surprised by is that computeMatrix is not summing values, but taking the average in each bin. You can change this with the <code>--averageTypeBins</code> option (the default is <code>mean</code>, you presumably want <code>sum</code>).</p>
  
  <p><strong>Update</strong>: For those wondering the cause of the confusion was due to not using <code>--missingDataAsZero</code>. In other words, including or not including NAs will lead to different results, since different numbers of values will be included.</p>
  