Hi, I saw from your lab's new published paper(https://www.biorxiv.org/content/10.1101/2020.02.26.966697v1.full) that
"First, we identified 58,988 and 49,258 loops in SCABER and SW780 cells respectively (prob>0.8). Then by using the probability score output from Peakachu, we defined subtype-specific chromatin loops, as shown in the Aggregate Peak Analysis".
Could you tell me how to define the specific chromatin loops? Do you just simply count the presence/absence of loops detected in both two samples?
Hi, I saw from your lab's new published paper(https://www.biorxiv.org/content/10.1101/2020.02.26.966697v1.full) that "First, we identified 58,988 and 49,258 loops in SCABER and SW780 cells respectively (prob>0.8). Then by using the probability score output from Peakachu, we defined subtype-specific chromatin loops, as shown in the Aggregate Peak Analysis".
Could you tell me how to define the specific chromatin loops? Do you just simply count the presence/absence of loops detected in both two samples?
Thanks! Yanchun