Question: How to use my own genome on UCSC browser?
0
gravatar for SmallChess
3.5 years ago by
SmallChess460
Australia
SmallChess460 wrote:

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.

browser next-gen genome • 1.7k views
ADD COMMENTlink modified 3.5 years ago by Leszek3.9k • written 3.5 years ago by SmallChess460
2
gravatar for Jennifer Hillman Jackson
3.5 years ago by
Bay Area, CA
Jennifer Hillman Jackson350 wrote:

Hello,

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:
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

 

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Jennifer Hillman Jackson350
1
gravatar for Dan D
3.5 years ago by
Dan D6.6k
Tennessee
Dan D6.6k wrote:

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.

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Dan D6.6k

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.

ADD REPLYlink written 3.5 years ago by Jennifer Hillman Jackson350
0
gravatar for Alex Reynolds
3.5 years ago by
Alex Reynolds26k
Seattle, WA USA
Alex Reynolds26k wrote:

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.

ADD COMMENTlink written 3.5 years ago by Alex Reynolds26k
0
gravatar for Leszek
3.5 years ago by
Leszek3.9k
IIMCB, Poland
Leszek3.9k wrote:

IGV / IGB are great if you are the only person analysing the data. 

In case you want to share the data with someone else ie collaborators, or your boss, have a look at jBrowse, it's really great! 

ADD COMMENTlink written 3.5 years ago by Leszek3.9k
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