Previously, I made a post on adding custom tracks to the UCSC Genome Broswer and have even expanded on coloring these tracks. For most of my applications, I have simply used standard .bed files that plot features of interest in the Genome Browser in relation to other UCSC tracks. Today I wanted to plot data from overlapping features in a depth plot similar to what one would see after next-generation sequencing. I found the easiest way to do this was by importaing a BedGraph file into the Genome Browser. Following steps similar to the custom tracks post, you go to the My Data -> Custom Tracks -> Add Custom Tracks and then upload the BedGraph file. Below is an example of what the header and the first few lines need to look like.
More details and options on the BedGraph track format can be found here on the UCSC webpage.
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