Answers.Body: <ol>
  <li>Your original command without <code>--nomodel --extsize ...</code> is probably the most accurate. This warning stems from a time when reads were much much shorter and likely never made that much sense to begin with.</li>
  <li>Broad peak calling in MACS2 basically works by finding a bunch of nearish narrow peaks and merging them. If you have really broad signals then use something like <code>histoneHMM</code> instead.</li>
  <li>H3K27ac, H3K4me1 and H3K4me3 are narrow. H3K27me3 is broad.</li>
  <li>Yeah, but you'll need to spend a bit more time with the data to ensure that the peaks are reasonable (you'll have to tweak the parameters if not).</li>
  </ol>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-14T14:11:23.530Z
Answers.Text: Adding to Devon Ryan's answer, see [this image](https://i.sstatic.net/olCjj.png) from [ENCODE](https://www.encodeproject.org/chip-seq/histone/).
Answers.UserDisplayName: EagleEye
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-07T18:52:02.940Z
Answers.LastActivityDate: 2018-06-07T18:52:02.940Z
Answers.UserDisplayName: Devon Ryan
Body: <p>I have paired end ChIP-seq data with 101 bp and 2 biological replicates for each one. I have done peak calling with macs2 but I have some questions about it.</p>
  
  <p>I also faced with an warning:</p>
  
  <blockquote>
    <p>WARNING @ Thu, 07 Jun 2018 17:06:05: #2 Since the d (197) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem!<br>
    WARNING @ Thu, 07 Jun 2018 17:06:05: #2 You may need to consider one of the other alternative d(s): 197<br>
    WARNING @ Thu, 07 Jun 2018 17:06:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. </p>
  </blockquote>
  
  <ol>
  <li><p>I have added <code>--nomodel --extsize 197 ; --nomodel --extsize 147</code> and <code>--nomodel --extsize 202</code> (separately to macs2 command) and got the results without any warning? Which one is more correct?</p></li>
  <li><p>Are broad peaks extended of narrow peaks? If I apply intersect between them I should expect find 100% overlap between narrow peaks and broad ones?</p></li>
  <li><p>Which kind of peak (narrow/broad) is proper for H3k27ac, H3k4me1, H3k4me3, H3k27me3 study?</p></li>
  <li><p>If there is no control group for using as background, can I use default parameters?</p></li>
  </ol>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-07T19:10:19.570Z
Comments.Text: cross posted: https://www.biostars.org/p/319418/
Comments.UserDisplayName: Pierre
Tags: <chip-seq>
Title: Macs2 peak calling?
ThreadText: # Macs2 peak calling?
  
  (Asked by: username_0 on 2018-06-07)
  
  I have paired end ChIP-seq data with 101 bp and 2 biological replicates for each one. I have done peak calling with macs2 but I have some questions about it.
  
  I also faced with an warning:
  
  > WARNING @ Thu, 07 Jun 2018 17:06:05: #2 Since the d (197) calculated from paired-peaks are smaller than 2\*tag length, it may be influenced by unknown sequencing problem!  
  > WARNING @ Thu, 07 Jun 2018 17:06:05: #2 You may need to consider one of the other alternative d(s): 197  
  > WARNING @ Thu, 07 Jun 2018 17:06:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing.
  
  1. I have added `--nomodel --extsize 197 ; --nomodel --extsize 147` and `--nomodel --extsize 202` (separately to macs2 command) and got the results without any warning? Which one is more correct?
  2. Are broad peaks extended of narrow peaks? If I apply intersect between them I should expect find 100% overlap between narrow peaks and broad ones?
  3. Which kind of peak (narrow/broad) is proper for H3k27ac, H3k4me1, H3k4me3, H3k27me3 study?
  4. If there is no control group for using as background, can I use default parameters?
  
  **Tags:** chip-seq
  
  > **Comments:**
  > **username_1**: cross posted: https://www.biostars.org/p/319418/  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2018-06-07. Score: 4 | Accepted answer
  
  1. Your original command without `--nomodel --extsize ...` is probably the most accurate. This warning stems from a time when reads were much much shorter and likely never made that much sense to begin with.
  2. Broad peak calling in MACS2 basically works by finding a bunch of nearish narrow peaks and merging them. If you have really broad signals then use something like `histoneHMM` instead.
  3. H3K27ac, H3K4me1 and H3K4me3 are narrow. H3K27me3 is broad.
  4. Yeah, but you'll need to spend a bit more time with the data to ensure that the peaks are reasonable (you'll have to tweak the parameters if not).
  
  > **Comments:**
  > **username_3**: Adding to username_2 username_2's answer, see [this image](https://i.sstatic.net/olCjj.png) from [ENCODE](https://www.encodeproject.org/chip-seq/histone/).  
  
  ---
  
  