text: user285: I would like to calculate what is the number of region which is lost or gained between two condition,such as Stem cell vs Leukemic stemcell, atac seq data. 
  How do I get the information after peak calling such as what tools should i be using ?
  As shown in the paper figure 1c I would like to do the same. How do i calculate the gain and loss of peak relative to a condition 
  paper
  
  user3541: What you are looking for is "Differential accessibility analysis", you are using ATAC-seq, hence "accessibility". You will need to "call" and then "normalize" "count"(*) peaks, after these, you can use DESeq2 or edgeR for the "differential" part.
  Here is a nice Nextflow workflow that addresses all of the steps of a differential accessibility analysis of ATAC-Seq data.
  * featureCounts can be used the identify peaks, see this and this.
  
original_text: 285: <p>I would like to calculate what is the number of region which is lost or gained between two condition,such as Stem cell vs Leukemic stemcell, atac seq data. </p>
  
  <p>How do I get the information after peak calling such as what tools should i be using ?</p>
  
  <p>As shown in the paper figure 1c I would like to do the same. How do i calculate the gain and loss of peak relative to a condition 
  <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0840-9" rel="nofollow noreferrer">paper</a></p>
   3541: <p>What you are looking for is "Differential accessibility analysis", you are using ATAC-seq, hence "accessibility". You will need to "call" and then <strike>"normalize"</strike> "count"(*) peaks, after these, you can use <code>DESeq2</code> or <code>edgeR</code> for the "differential" part.</p>
  
  <p><a href="https://github.com/nf-core/atacseq" rel="nofollow noreferrer">Here is a nice Nextflow workflow</a> that addresses all of the steps of a differential accessibility analysis of ATAC-Seq data.</p>
  
  <p>* <code>featureCounts</code> can be used the identify peaks, see <a href="https://support.bioconductor.org/p/103059/" rel="nofollow noreferrer">this</a> and <a href="https://support.bioconductor.org/p/120013/" rel="nofollow noreferrer">this</a>.</p>
  