<p>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.</p>

<p>I envisage the input would be a bedGraph/Wig file and a list of binding region coordinates.  I am aware of a previous <a href='http://www.biostars.org/p/6132/#6138'>Biostars thread</a> 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.  </p>

<p>I wonder whether some Python guru etc. has already tackled this?</p>

<p>Many thanks!</p>

<p>I will like to update my previous answer:</p>

<p>We have made available a suite of tools called <a href='http://deeptools.github.io'>deepTools</a> to make this sort of visualizations very easy. There is a tool called profiler that will plot exactly what you want. You provide a list of regions (BED or GFF format) and a bigWig file and the output is a profile. <a href='https://github.com/fidelram/deepTools/wiki/Visualizations'>Here</a> you can find the documentation on how to run the tool. You can easily convert any wig/bedgraph file to a bigWig using the tools from UCSC that can dowloaded here: <a href='http://hgdownload.cse.ucsc.edu/admin/exe/'>http://hgdownload.cse.ucsc.edu/admin/exe/</a></p>

<p>The tool uses bigWig files to parallelize computations. </p>

<p><img src='https://raw.github.com/fidelram/deepTools/master/examples/flowChart_computeMatrixetc.png' alt='enter image description here' /></p>
