merge replicate for bigWig files from macs2 peak calling
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?
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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)