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.
A repository of programs, scripts, and tips essential to
genetic epidemiology, statistical genetics, and bioinformatics
Welcome to the Genome Toolbox! I am glad you navigated to the blog and hope you find the contents useful and insightful for your genomic needs. If you find any of the entries particularly helpful, be sure to click the +1 button on the bottom of the post and share with your colleagues. Your input is encouraged, so if you have comments or are aware of more efficient tools not included in a post, I would love to hear from you. Enjoy your time browsing through the Toolbox.
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