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't have to be the UCSC browser.
Galaxy (http://usegalaxy.org) 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:
Details & Troubleshooting: http://wiki.galaxyproject.org/Learn/CustomGenomes
Hopefully this will work out for you, Jen, Galaxy team
Use IGV. It's a java desktop application, so it's platform-independent. It's very easy to load your own reference in FASTA format, along with gene annotations. I do it all the time.
There's also IGB, which is great as well.
Another option is to run a local server with the WashU Epigenome Browser installed. You can add custom genomes to it and integrate data from UCSC services. It offers some visualization options that other browsers do not.