Answers.Body: <p>I'd say mostly this is a question of understanding the underlying biology and the relevant literature. </p>
  
  <p>If it is not known in the literature whether a mark is peaky or broad, evidence might come from FISH studies or Low throughput qPCR. Another way to look would be to examine the signal expressed as fold enrichment over input on a genome browser and look if peaks tended to be small (a few hundred bp, e.g. a transcription factor), or large (several 1kb, e.g. H3K27me3) or contain both (e.g. RNA polymerase II). </p>
  
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Answers.Text: That makes sense, but H3K27ac is frequently thought to be broad and the peaks look broad, but is apparently narrow.
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Answers.Text: Always these things are going to be a judgement call. There are going to be marks that some people count as braod that others count as narrow, and vice versa.
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Answers.UserDisplayName: Ian Sudbery
Body: <p>Is there a method to determine if the peaks are broad or narrow? ENCODE provides some <a href="https://www.encodeproject.org/chip-seq/histone/" rel="nofollow noreferrer">guidelines</a>:</p>
  
  <p><a href="https://i.sstatic.net/VanZO.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/VanZO.png" alt="histone peak size"></a></p>
  
  <p>Although those cover common histone marks, there are many others. If you are using one of the ones that are not listed, is there a way to determine the appropriate peak width?</p>
  
  <p>This question was inspired by <a href="https://bioinformatics.stackexchange.com/a/4450/35">this previous post</a>.</p>
  
Tags: <chip-seq><peak-calling>
Title: determine if ChIP-seq peaks are broad or narrow
ThreadText: # determine if ChIP-seq peaks are broad or narrow
  
  (Asked by: username_0 on 2018-06-14)
  
  Is there a method to determine if the peaks are broad or narrow? ENCODE provides some [guidelines](https://www.encodeproject.org/chip-seq/histone/):
  
  [![histone peak size](https://i.sstatic.net/VanZO.png)](https://i.sstatic.net/VanZO.png)
  
  Although those cover common histone marks, there are many others. If you are using one of the ones that are not listed, is there a way to determine the appropriate peak width?
  
  This question was inspired by [this previous post](https://bioinformatics.stackexchange.com/a/4450/35).
  
  **Tags:** chip-seq, peak-calling
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2018-06-20. Score: 3
  
  I'd say mostly this is a question of understanding the underlying biology and the relevant literature.
  
  If it is not known in the literature whether a mark is peaky or broad, evidence might come from FISH studies or Low throughput qPCR. Another way to look would be to examine the signal expressed as fold enrichment over input on a genome browser and look if peaks tended to be small (a few hundred bp, e.g. a transcription factor), or large (several 1kb, e.g. H3K27me3) or contain both (e.g. RNA polymerase II).
  
  > **Comments:**
  > **username_0**: That makes sense, but H3K27ac is frequently thought to be broad and the peaks look broad, but is apparently narrow.  
  > **username_1**: Always these things are going to be a judgement call. There are going to be marks that some people count as braod that others count as narrow, and vice versa.  
  
  ---
  
  