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kundajelab / atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline
BSD 3-Clause "New" or "Revised" License
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Is there any difference between Conservative Set and Optimal Set of peaks? #117

Closed amirshams84 closed 6 years ago

amirshams84 commented 6 years ago

I don't see any difference

leepc12 commented 6 years ago

Those sets don't have to be always different.

How many replicates did you run pipelines with? If it's just one, those two sets should be identical.

Jin

On Wed, May 23, 2018 at 8:18 AM, amirshams notifications@github.com wrote:

I don't see any difference

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akundaje commented 6 years ago

The optimal set is the maximal set of peaks one can get by comparing true replicates or pseudoreplicates (obtained by pooling reads from true replicates and subsampling equal number of mutually exclusive reads). So some times they can be the same. And they will be the same if there is only one replicate.