What advanced parameters which need to be set for analysing ATAC seq replicates using edgeR in usegalaxy.org ?

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What advanced parameters which need to be set for analysing ATAC seq 4 healthy and 4 diseased replicates in edgeR

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Hi @Mercy_Stephen,
according this paper, you should use the following parameters:

  • Use Robust Settings
  • Use Likelihood Ratio Test

Here is the original R code.

Regards

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