merge replicate for bigWig files from macs2 peak calling

Question

[QX]

Hi all,

I have ATAC-seq data which many conditions and 2 replicates for each. I have perform DEseq2 to detect the differentially accessibility peaks. Now I using deeptools plotHeatmap to plot for each condition (based on the DEseq2 outcome peaks).

Is it more preferable to plot 2 replicates separately (which I think is redundant) or shall I combine the 2 bigwig replicate files and plot. How can I do the merge for 2 bigWig files? and will it take the mean or the sum of two files?

[ATpoint]

For these sorts of plot taking the mean between replicates is usually what I do. Biological replication is not "redundant" but for these sorts of plots it can be tedious. See also Average bigwig files (not sum)