In ChIP-seq. analysis, what is the proper way to combine biological replicates for signal profile plotting?
At the moment, I'm using deepTools
plotProfile to visualize the signal density around TSS. After plotting the replicates separately, I can see that they are highly similar. Then, I would like to pool the replicates and presenting them as one single line in the profile. Should I achieve this by merging the bigWig files (e.g.
bigWigMerge from UCSC tools as suggested by Devon in this post?) generated from
bamCompare? (Each of the replicates has been compared to their own input in bamCompare & normalized to 1x Reads Per Genomic Content (RPGC).