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.

Tuesday, May 28, 2013

Custom Tracks in UCSC Genome Browser

One of my colleagues recently shared a web link to a custom track they had uploaded and visualized on the standard UCSC Genome Browser.  A bit impressed, I looked into how to do this myself.  UCSC has a pretty informative webpage detailing how to add custom tracks to Genome Browser.  Here's a quick summary of what you need to do.

First get your data in one of the formats supported by Genome Browser (.gtf, .gff, .bed, .wig, or .psl).  I usually prefer .bed when appropriate.  Next login to your account on Genome Browser.  If you don't have an account, sign up for a free one here.  Then go to the UCSC Add Custom Tracks link.  Select the appropriate genome and assembly and then upload your data under the "Paste URLs or data" section.  After pressing Submit, it will take you to a new page where you will see that your new track is generated and where you can follow a link to see it in the Genome Browser.  You can now explore how other tracks match up to your custom track.  You can also save your session and share it with others by creating a URL link to it.  Here is an example of a custom track I made from FASTA files where I wanted to compare gaps in FASTA files to the Gaps track at UCSC.  Have fun with custom tracks on UCSC Genome Browser.

No comments:

Post a Comment