Answers.Body: <p>You can use <code>Homer</code> to retrieve tag densities, quoting from their <a href="http://homer.ucsd.edu/homer/ngs/quantification.html" rel="nofollow noreferrer">manual</a>:</p>
  
  <blockquote>
    <p><strong>Calculating ChIP-Seq Tag Densities across different experiments</strong></p>
    
    <p>annotatePeaks.pl is [a] useful program for cross-referencing data from
    multiple experiments.  In order to count the number of tags from
    different sequencing experiments, you must first create tag
    directories for each of these experiments.  Once created, tag counts
    from these directories in the vicinity of your peaks can be added by
    specifying "-d   ...".  You can
    specify as many tag directories as you like.  Tag totals for each
    directory will be placed in new columns starting on column 18.  For
    example:</p>
    
    <p>annotatePeaks.pl pu1peaks.txt mm8 -size 400 -d Macrophage-PU.1/
    Bcell-PU.1/ > output.txt</p>
  </blockquote>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-10-23T10:51:47.047Z
Answers.Text: Out of curiosity, what is actually? Reads per base pair?
Answers.UserDisplayName: StupidWolf
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Answers.CreationDate: 2019-10-23T11:01:40.960Z
Answers.Text: @StupidWolf, I cannot seem to understand the question, could you please provide more context?
Answers.UserDisplayName: haci
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Answers.Text: Sorry @haci typed too fast, I meant what is "tag density" exactly. I don't use Homer, so when I read the publication pointed out in the original question, I assume it's something like reads per bp of the peak?
Answers.UserDisplayName: StupidWolf
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Answers.Text: In my understanding it is the number of reads in a given genomic region or peak, in that respect it would be analogous to gene counts. I also found a similar [Q&A on this:](http://seqanswers.com/forums/showthread.php?t=74730)
Answers.UserDisplayName: haci
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Answers.Text: I finally landed up here http://homer.ucsd.edu/homer/ngs/quantification.html
Answers.UserDisplayName: kcm
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Answers.UserDisplayName: haci
Body: <p>I m quoting this  <a href="https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(17)30429-0?innerTabgraphical_S1934590917304290=" rel="nofollow noreferrer">paper</a> <a href="https://i.sstatic.net/9gJFl.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/9gJFl.jpg" alt="figure"></a>, figure B where they write </p>
  
  <p>"B) Violin plots for the normalized ATAC-seq <strong><em>tag density</em></strong> for all peaks within the indicated OC/CO groups at the indicated time points. Data were converted to a Z score based on the row-wise SD for each peak. ∗p &lt; 0.01 Mann-Whitney U test." </p>
  
  <p>My question is where is this tag density information coming from.</p>
  
  <p>So far for chipseq data what I have done is</p>
  
  <ul>
  <li>Aligned the data</li>
  <li>Then all required data processing post alignment </li>
  <li>Generated bed and bigwig files of respective samples required for comparison</li>
  <li>Made tag-directory using homer.</li>
  <li>Then peak-calling using homer,annotated peak using homer.</li>
  </ul>
  
  <p>Now so far I am not able to figure out where is this tag-density information is .</p>
  
  <p>Any help or suggestion would be really appreciated.</p>
  
Tags: <chip-seq>
Title: Tag density plot form chip or atac seq data
ThreadText: # Tag density plot form chip or atac seq data
  
  (Asked by: username_0 on 2019-10-23)
  
  I m quoting this [paper](https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(17)30429-0?innerTabgraphical_S1934590917304290=) [![figure](https://i.sstatic.net/9gJFl.jpg)](https://i.sstatic.net/9gJFl.jpg), figure B where they write
  
  "B) Violin plots for the normalized ATAC-seq ***tag density*** for all peaks within the indicated OC/CO groups at the indicated time points. Data were converted to a Z score based on the row-wise SD for each peak. ∗p < 0.01 Mann-Whitney U test."
  
  My question is where is this tag density information coming from.
  
  So far for chipseq data what I have done is
  
  * Aligned the data
  * Then all required data processing post alignment
  * Generated bed and bigwig files of respective samples required for comparison
  * Made tag-directory using homer.
  * Then peak-calling using homer,annotated peak using homer.
  
  Now so far I am not able to figure out where is this tag-density information is .
  
  Any help or suggestion would be really appreciated.
  
  **Tags:** chip-seq
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-10-23. Score: 2
  
  You can use `Homer` to retrieve tag densities, quoting from their [manual](http://homer.ucsd.edu/homer/ngs/quantification.html):
  
  > **Calculating ChIP-Seq Tag Densities across different experiments**
  >
  > annotatePeaks.pl is [a] useful program for cross-referencing data from
  > multiple experiments. In order to count the number of tags from
  > different sequencing experiments, you must first create tag
  > directories for each of these experiments. Once created, tag counts
  > from these directories in the vicinity of your peaks can be added by
  > specifying "-d ...". You can
  > specify as many tag directories as you like. Tag totals for each
  > directory will be placed in new columns starting on column 18. For
  > example:
  >
  > annotatePeaks.pl pu1peaks.txt mm8 -size 400 -d Macrophage-PU.1/
  > Bcell-PU.1/ > output.txt
  
  > **Comments:**
  > **username_2**: Out of curiosity, what is actually? Reads per base pair?  
  > **username_1**: @username_2, I cannot seem to understand the question, could you please provide more context?  
  > **username_2**: Sorry @username_1 typed too fast, I meant what is "tag density" exactly. I don't use Homer, so when I read the publication pointed out in the original question, I assume it's something like reads per bp of the peak?  
  > **username_1**: In my understanding it is the number of reads in a given genomic region or peak, in that respect it would be analogous to gene counts. I also found a similar [Q&A on this:](http://seqanswers.com/forums/showthread.php?t=74730)  
  > **username_0**: I finally landed up here http://homer.ucsd.edu/homer/ngs/quantification.html  
  
  ---
  
  