Question: Difference between "peaks" and "hotspots" in Output.type of ENCODE DNase-seq data sets
gravatar for panyard
20 months ago by
panyard10 wrote:

I'm having trouble understanding the difference between two types of "Output.type" for DNase-seq data sets from ENCODE. About half of them are labeled as "peaks" and the other half as "hotspots". Looking through the ENCODE website ( (, I can see that Hotspot is the name of a program that is used in the analysis pipeline, but I don't see any description of the difference between hotspots and peaks as output types. The only difference I did see was that all hotspots were for bed broadPeak files and all peaks were for bed narrowPeak files, so perhaps this is just inconsistency in the naming convention?

Does anyone know if there's any real difference between these Output.type designations? Thanks

hotspots dnase-seq peaks encode • 1.4k views
ADD COMMENTlink modified 20 months ago by Alex Reynolds27k • written 20 months ago by panyard10
gravatar for Alex Reynolds
20 months ago by
Alex Reynolds27k
Seattle, WA USA
Alex Reynolds27k wrote:

Hotspots are areas of enriched DNaseI cleavage called on full or subsampled read sets. Peaks are 150nt regions that overlap or are contained within hotspots, which are areas of very high density relative to background. These 150nt regions are also called DHSs (DNase-hypersensitive sites). This is for first-generation hotspot data. The hotspot2 method calls variable-sized DHSs.

ADD COMMENTlink modified 20 months ago • written 20 months ago by Alex Reynolds27k
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