Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-11-29T20:59:33.423Z
Answers.LastActivityDate: 2018-11-29T20:59:33.423Z
Answers.UserDisplayName: James Hawley
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-26T11:34:55.833Z
Comments.Text: This is going to be an custom script so you're not going to touch MACS2 itself. The only question is how you want to summarize q-values from different samples. Other than that this is a job for bedtools/bedops.
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-27T14:51:24.687Z
Comments.Text: Here's why I think I still need MACS - say Sample A has a peak at chrN:100-200, but Sample B does not. In order to avoid missing values, I would like to get the (not significant) enrichment score from that peak for Sample B using the MACS2 algorithm.
Comments.UserDisplayName: Scott Gigante
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-27T15:04:57.653Z
Comments.Text: Ah, if you really want that then yes you'll need to use the (undocumented) MACS2 API.
Comments.UserDisplayName: Devon Ryan
Tags: <chip-seq><peak-calling><macs2>
Title: Score predefined ChIP-seq peaks with MACS2 or equivalent
ThreadText: # Score predefined ChIP-seq peaks with MACS2 or equivalent
  
  (Asked by: username_0 on 2018-11-26)
  
  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?
  
  **Tags:** chip-seq, peak-calling, macs2
  
  > **Comments:**
  > **username_1**: This is going to be an custom script so you're not going to touch MACS2 itself. The only question is how you want to summarize q-values from different samples. Other than that this is a job for bedtools/bedops.  
  > **username_0**: Here's why I think I still need MACS - say Sample A has a peak at chrN:100-200, but Sample B does not. In order to avoid missing values, I would like to get the (not significant) enrichment score from that peak for Sample B using the MACS2 algorithm.  
  > **username_1**: Ah, if you really want that then yes you'll need to use the (undocumented) MACS2 API.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2018-11-29. Score: 2
  
  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.
  
  
  ---
  
  