<p>I have created my own genome for research. I have data for this fake genome. Now I want compare this genome with a BAM file on UCSC or any other browser. However, the browser only allows me to select a known genome as the reference. How do I provide my own genome on a browser, it doesn&#39;t have to be the UCSC browser.</p>

Hello,

[Galaxy][1] has a very robust "Custom Reference Genome" feature that functions with both analysis tools and visualization. This permits nearly any fasta file to be used as a reference genome. **Galaxy's visualization browser is called "Trackster".**

Start by loading the fasta file of your "fake" genome. From there it can be directly used with tools. To go forward and use this genome with Trackster, create a "Custom Build" based on the fasta version of the genome. All of this takes a few minutes to do at most. Full instructions, including help videos, are in the http://galaxyproject.org wiki here:
Summary: http://wiki.galaxyproject.org/Support#Custom_reference_genome
Details & Troubleshooting: http://wiki.galaxyproject.org/Learn/CustomGenomes

Hopefully this will work out for you, Jen, Galaxy team

 [1]: http://usegalaxy.org