A question about the enriched cCRE

[chiayic]

Hello,

My question is about the calculation behind the enrichment for cCREs or motifs. I understand that your lab has been continuously developing software tools to find TFBS/clusters in DNA sequences, such as CLOVER, Cluster-Buster, and others. I was wondering:

1. If you have a current preferred tool (Is it Cluster-Buster, as mentioned on the website?);
2. What's the method used in ENCODE-cCRE. Specifically, I’m curious about the input for the fisher-test-tf-motif-fcc.py (Line 18). It seems like the script is counting the presence/absence of motifs, rather than coverage or probability—am I misunderstanding this?

Thank you so much for the time and the wonderful resource!