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!
I was thinking per-base variance, though sliding window would also work to alert of high variance between replicate. Using R, I make average coverage plots ± variance for individual genes, but I do not have a tool/GUI to actively browse the genome. So, it requires me to identify interesting genes through other mechanisms and then create plots of said genes. It's pretty wasteful: time consuming to run, occupies lots of HD space, and end up pitching many plots that end up being uninteresting.
Thank you for the suggestions about tools. I have no experience in GUI development and don't think that's a journey I'll embark on at the moment.