I often have ChIP-seq experiments where I want to get a feel for read coverage over the predicted binding regions. Looking through the UCSC genome browser region by region is slow and labourious. What i am looking for is a way of plotting read coverage (from bedGraph, Wig etc) for many different binding regions and present many of these plots on one page.
I envisage the input would be a bedGraph/Wig file and a list of binding region coordinates. I am aware of a previous Batch Viewing Of Ucsc Browser Graphic that kind of covers this, but it uses UCSC/IGV. I am looking for something much more simplistic - just a line graph per region. Even more, it would be great to be able to plot ChIP and input read coverage on the same graph.
I wonder whether some Python guru etc. has already tackled this?