The Integrative Genomics Viewer

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Genome browsers are great. The UCSC Genome Browser is probably the King of the Browsers (unless you're an Arabidopsis person, in which case it's Annoj), but those guys are a little stuck-up and won't host the X. laevis genome yet. This is a shame, because even the current X. laevis v7b build is way better (n50 of ~3.5 Mb) than lots of genomes already on UCSC (The gorilla n50 is only 1 Mb? Please).


That's okay, there are lots of other options. Xenbase likes gBrowse, while I am a real fan of IGV. So go on down to the site and take it for a spin.


There are two major ways to use it.

1. You can click a button on the site to launch the browser ("Java web start"), which is great for your first time. You can pick a few different options for memory. Depending on what kind of data you're loading, you could get away with a modest option, but if you start loading lots of bams or bedGraphs you're going to run out of memory real quick. Also, if you're using a Mac, Apple Computers is real anal about Java and it's quite possible that your Mac won't want to run Java, even the newest release (turns out Java is a real easy way to sneak into other peoples' computers). So, if that happens, or if you want a little more control over the browser, try the second option.


2. Install IGV on your own machine and run it from there.