Do I need to remove ATAC-Seq large peaks?

Hello, I am doing ATAC-Seq analysie. I checked peaks size after runing genrich (-j) peak calling. Let's say my peaksets is peaks1 (control) and peaks2 (treatment).

> summary(width(peaks1))
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  101.0   242.0   397.0   532.5   648.0 59816.0 
> summary(width(peaks2))
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  106.0   241.0   367.0   479.7   573.0 59843.0

We can see there is some large peaks, is this normal that cells have some large open chromatin, do I need to remove them with some threshold? For example remove peaks "> 1200bp".

atac-seq genrich

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written 4.6 years ago by MatthewP

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