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.

Generate URLs to Share Genome Browser Sessions

Its happened to me several times before.  I spend several minutes zooming in on a region of interest and selecting all the tracks I want to see on Genome Browser, but have no great way of sharing the session with a colleague.  I usually do a print screen and email a copy of the screenshot, but then they have no way of manipulating the view themselves.  I always think in the back of my head that there must be a better way to do this.  Well, the good news is there is!

Today I stumbled across a way to generate a URL link to what Genome Browser calls a "session".  A session is zoomed in view of a genomic region that contains all the tracks one is interested in.  These sessions can easily be saved and then shared with a colleague with a web link.  All you really need is a UCSC Genome Browser account.  If you don't have one, you can sign up here.

Once you have an account, go to the My Data (or Sessions...depending on what page you are on) tab on the header of the Genome Browser webpage.  Click Login and enter your username and password.  Then go back to the genome browser and zoom in on your region and pick the tracks you want to display.  When you get things picture perfect and ready to share, click on the My Data tab again, and select Sessions.  Go to Save Settings and under "Save current settings as named session" insert a name, check the box next to allow this session to be loaded by others, and press submit.  This will save the session and under My Sessions you should see the session you just saved.  You can right click on the Browser link next to the session name you just created and copy the link address to share with your colleagues.  Here is an example I made that displays common SNPs in the 8q24.21 region.  Happy URL sharing!