Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-19T12:49:21.443Z
Answers.Text: "You will need to "call" and then "normalize" peaks" this part im done. I tried with diffbind, but i was not sure about the result output clearly. Yes will check the nexflow one which i did see but haven;t tried it yet
Answers.UserDisplayName: kcm
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-19T13:04:40.183Z
Answers.Text: I think I was wrong about the normalization part. `DESeq2` and `edgeR` works on raw counts so I believe you will need to use `featureCounts` to get the counts to feed into one of the two DE tools.
Answers.UserDisplayName: haci
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-19T13:07:38.623Z
Answers.Text: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6527694/#MOESM2" preclisely yes they need raw count and how do i get raw counts from peaks? i ran deseq2 from rna seq data using raw count from bam files , i guess i can't do the same for ATAC seq ,need to get the counts from the peaks isn;t it?
Answers.UserDisplayName: kcm
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-19T13:15:54.997Z
Answers.Text: You can use `featureCounts`, I am editing my answer so as to include two links from the `Bioconductor` forum.
Answers.UserDisplayName: haci
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-17T17:26:25.317Z
Answers.Text: I manage to get differential peak analysis using deseq2 , now back to my original question now I do have differential peak between various stages how do I define the loss and gain of peaks between stages from deseq2 results or I have to use bedtool or bedops in this case ?
Answers.UserDisplayName: kcm
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-17T19:12:20.627Z
Answers.Text: I don't really understand your question as `DESeq2` output should be giving you what regions are more (or less) open (accessible) in one condition with respect to another (reference) condition. How does the `DESeq2` output look like, can you post the first few lines by editing your question?
Answers.UserDisplayName: haci
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-18T04:51:35.733Z
Answers.Text: " output should be giving you what regions are more (or less) open (accessible) in one condition with respect to another (reference) condition." yes the deseq2 will show differential accessibility . My question is how do i define loss and gain of peak with respect to reference sample
Answers.UserDisplayName: kcm
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-18T06:19:07.950Z
Answers.Text: updated the question
Answers.UserDisplayName: kcm
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-19T11:24:08.090Z
Answers.LastActivityDate: 2020-02-17T19:23:12.040Z
Answers.LastEditDate: 2020-02-17T19:23:12.040Z
Answers.UserDisplayName: haci
Body: <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>
  
Tags: <atac-seq>
Title: Loss and gain of region in ATAC seq
ThreadText: # Loss and gain of region in ATAC seq
  
  (Asked by: username_0 on 2019-11-19)
  
  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](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0840-9)
  
  **Tags:** atac-seq
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-11-19. Score: 3 | Accepted answer
  
  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](https://github.com/nf-core/atacseq) that addresses all of the steps of a differential accessibility analysis of ATAC-Seq data.
  
  \* `featureCounts` can be used the identify peaks, see [this](https://support.bioconductor.org/p/103059/) and [this](https://support.bioconductor.org/p/120013/).
  
  > **Comments:**
  > **username_0**: "You will need to "call" and then "normalize" peaks" this part im done. I tried with diffbind, but i was not sure about the result output clearly. Yes will check the nexflow one which i did see but haven;t tried it yet  
  > **username_1**: I think I was wrong about the normalization part. `DESeq2` and `edgeR` works on raw counts so I believe you will need to use `featureCounts` to get the counts to feed into one of the two DE tools.  
  > **username_0**: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6527694/#MOESM2" preclisely yes they need raw count and how do i get raw counts from peaks? i ran deseq2 from rna seq data using raw count from bam files , i guess i can't do the same for ATAC seq ,need to get the counts from the peaks isn;t it?  
  > **username_1**: You can use `featureCounts`, I am editing my answer so as to include two links from the `Bioconductor` forum.  
  > **username_0**: I manage to get differential peak analysis using deseq2 , now back to my original question now I do have differential peak between various stages how do I define the loss and gain of peaks between stages from deseq2 results or I have to use bedtool or bedops in this case ?  
  > **username_1**: I don't really understand your question as `DESeq2` output should be giving you what regions are more (or less) open (accessible) in one condition with respect to another (reference) condition. How does the `DESeq2` output look like, can you post the first few lines by editing your question?  
  > **username_0**: " output should be giving you what regions are more (or less) open (accessible) in one condition with respect to another (reference) condition." yes the deseq2 will show differential accessibility . My question is how do i define loss and gain of peak with respect to reference sample  
  > **username_0**: updated the question  
  
  ---
  
  