ATAC-seq analysis


I have two (maybe stupid questions). I have ATAC seq data from multiple groups each 3 replicates.

  1. How can I reach the normalization like in IDR (high confidence set) of the narrow peak files for 3 replicates?
  2. Is DiffBind working for multiple group comparisons? I tried to click on the insert group button but it doesn’t work. Is there another tool/flow that you would recommend for multiple group comparisons?

Thanks for the help

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Welcome @OmarMossad

Sorry for the delayed reply. Try reviewing your methods to those in the GTN tutorial that covers ATAC-seq analysis: