text: user163: I have performed peak calling on a number of separate ChIP-seq experiments and would like to harmonise the peaks from each of the experiments in order to convert my data into a matrix for further analysis. I would like to do this by taking the union of the called peaks (available in BED / narrowPeak / MACS2 format) and retrieving the enrichment score / q-value for all of the experiments on each peak. Is this possible without writing my own extension to MACS2?
  
  user240: You could try setting a high p-value threshold when you're calling peaks to retain the "non-significant" values. Something like:
  macs2 callpeak -t <ChIP>.bam -c <Control>.bam -f BED -g hs -n test -B -p 0.7
  
  You probably don't want to set the threshold to 1, since you'll likely want to avoid some noise.
  But you can then use these "non-significant" values in combination with a bedtools map command, to map them to your predefined union of "actual" peaks.
  
original_text: 163: <p>I have performed peak calling on a number of separate ChIP-seq experiments and would like to harmonise the peaks from each of the experiments in order to convert my data into a matrix for further analysis. I would like to do this by taking the union of the called peaks (available in BED / narrowPeak / MACS2 format) and retrieving the enrichment score / q-value for all of the experiments on each peak. Is this possible without writing my own extension to MACS2?</p>
   240: <p>You could try setting a high p-value threshold when you're calling peaks to retain the "non-significant" values. Something like:</p>
  
  <pre><code>macs2 callpeak -t &lt;ChIP&gt;.bam -c &lt;Control&gt;.bam -f BED -g hs -n test -B -p 0.7
  </code></pre>
  
  <p>You probably don't want to set the threshold to 1, since you'll likely want to avoid some noise.</p>
  
  <p>But you can then use these "non-significant" values in combination with a <code>bedtools map</code> command, to map them to your predefined union of "actual" peaks.</p>
  