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.
Hello,
Galaxy 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
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written
by
Jennifer Hillman Jackson
Another good choice. Data from Galaxy is also easily visualized within both IGV and IGB. For known genomes, the links are provided in the UI. So if you decide that you want to do some analysis along with the visualization, using both is an option.
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.
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written
by
Alex Reynolds
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