I have recently presented some ChIPseq data and one of the criticisms I received was the issue of having sufficient coverage in inferring peaks. I have two biological replicates (different donors) and the data looks very convincing to me due to good inter-donor reproducibility. For the purposes of simplicity I presented the genome-wide distribution of peaks (and their relative heights) on each chromosome and there were some arms of chromosomes that had no observable signal. This lack of signal I saw for each donor separately (independent analyses) and hence my confidence.
Nevertheless my conclusion was questioned on the basis of possible lack of sufficient coverage due to stochastic (random) forces and biases in library preparation. I think it rather unlikely that the same region would appear negative in two independent samples (with independent sequencing) due to stochastic bias. However I want to prove my point and show that I have good (background + ChIP signal) coverage across the genome.
Can you advise me with some software that could calculate coverage and ideally if it can draw some kind of histogram to see how uniform the sequencing across the genome was?