I am viewing BAM/bigwig files from ChIP-seq experiments. Every experiment has 3 biological replicates. Are there any tools that will plot the average coverage from replicates with a measure of variance? I have too many conditions and viewing any more than 9 individual tracks just isn't feasible.
I'm sure I could create a 'dummy' BAM/bigwig where I calculate the average coverage myself, and that would be compatible with viewers such as IGV. However, I'd really like to have a measure of variance included in the plot so I am alerted of potential issues with reproducibility amongst replicates.
Are there any programs that can do this? Thanks!