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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

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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.

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  • $\begingroup$ "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 $\endgroup$
    – kcm
    Nov 19 '19 at 12:49
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    $\begingroup$ 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. $\endgroup$
    – haci
    Nov 19 '19 at 13:04
  • $\begingroup$ "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? $\endgroup$
    – kcm
    Nov 19 '19 at 13:07
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    $\begingroup$ You can use featureCounts, I am editing my answer so as to include two links from the Bioconductor forum. $\endgroup$
    – haci
    Nov 19 '19 at 13:15
  • $\begingroup$ 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 ? $\endgroup$
    – kcm
    Feb 17 '20 at 17:26

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