text: user285: I m quoting this  paper , 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.
  
  user3541: You can use Homer to retrieve tag densities, quoting from their manual:
  
  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
  
  
original_text: 285: <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.stack.imgur.com/9gJFl.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/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>
   3541: <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>
  