MACS2 , heatmap

Question

[qudrat.nii]

Hello guys, I am doing cut&run analysis for some transcription factors and I have three replicates of BAM files and three replicates of MACS2 output. For downstream studies should I merge three replicates of bam file to plot heatmap? In case replicates are not highly correlated what should I do?

[ATpoint]

That depends what 'downstream analysis' is. You're asked some questions related to this snd in none I see details in the analysis goals.